Hey hey everyone, just an update, sorry for the delay I really wanted to make sure this issue was fixed until I reported back.
It seems that the issue was the front cylinder wasn't firing fully or as efficiently as it should've. Air was good, compression was good, plugs were fine but when the carbs were taken apart the main pilot jet had such debris. My theory is that the fuel system was so filthy that until the petcock, pump and carbs were cleaned (in that order) the pilot jet would just get fouled no matter what. I am riding quite happily on my bike and now can stare into the abyss of mods, upgrades and creature features. Thanks guys!