After lots of hours delving into this problem I have fixed it by using pipe:/// to ffmpeg in tvheadend muxes. Using HdHomerun Prime (with cable card) as source.
EG:
In the "URL:" section of Muxes
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v528 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
You can automate adding all of these by making an HDHomerunPrime1.m3u file (like below) adding in "Networks Tab" a new "IPTV Automatic Network" and providing a link to your m3u file in the "URL:" section of your new network.
#EXTM3U
#EXTINF:-1,[USAeHD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v524 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[AMCeHD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v525 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[MTVeHD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v526 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[CNNHD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v527 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[A&EeHD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v528 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[TWCHD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v529 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[ESPN2HD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v530 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[ESPNHD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v531 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[TLCeHD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v533 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[TNTeHD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v534 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[FNCHD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v535 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[E!eHD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v536 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[TRVLeHD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v537 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[CMTeHD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v538 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[TCMHD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v540 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[NICKeHD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v541 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[ANPLeHD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v542 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[TBSeHD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v543 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[SYFYeHD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v544 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[FOODeHD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v547 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[DISCeHD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v548 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[HGTVeHD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v549 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[HISTeHD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v550 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[ALTUTHD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v551 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[FAMwHD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v555 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[CNBCHD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v557 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[VH1eHD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v558 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[CMDYwHD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v559 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[HALLeHD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v560 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[TRUeHD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v561 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[FXwHD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v563 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[MNBCHD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v564 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[OXYGeHD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v566 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[E-Vine HD (Shop]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v573 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[JWLY HD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v575 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[MTV 2 HD east]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v577 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[TVLD HD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v579 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[ID HD e]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v580 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[BET HD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v581 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[BRVOeHD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v582 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[LIFEe HD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v584 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[FX Movie Channe]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v593 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[HALLMARK MOVIE]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v594 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[DISNEY XD HD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v602 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[Bloomberg HD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v613 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[HLN HD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v614 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[FOX BUSINESS HD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v615 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[CSPAN HD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v617 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[CSPAN2 HD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v618 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[CSPAN3 HD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v619 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[NBC SPORTS HD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v646 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[FXX HD east]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v647 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[OUTDOOR HD east]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v650 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[FOX SPORTS 1 HD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v652 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[Fox Sports 2 HD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v653 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[ALT2HD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v654 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[NATIONAL GEO HD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v665 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[Liquidation HD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v677 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[Son Life HD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v678 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
#EXTINF:-1,[VLCTYHD]
pipe:///usr/bin/ffmpeg -loglevel fatal -i http://10.7.7.100:5004/auto/v801 -vcodec libx264 -preset superfast -vf yadif=0,scale=-2:720 -b:v 2600k -acodec aac -b:a 128K -copyinkf -f mpegts pipe:1
This works really well, I no longer choke on more than 4 streams and my CPU will go all the way to 100% @ 6 streams at the same time. Now I just need better hardware to be able to transcode all 9 tuners (2/3 the way there with an i7-3770). Not sure what the problem is with TVH as far as not being able to do more than 4 streams with the built in method and libav on this hardware but, this works. Hopefully someone will find this useful in the future and save themselves a bunch of time.
Cheers