Ok, Update on this problem. I have cleaned the IAC, it was perfectly clean to begin with. Started the bike with it out and watched it function. Seems to be working as designed. I replaced the TPS, I did a test on the OHM reading while rotating it from open to closed. I used a meter with a graph. The signal would spike up and back down at one point in both directions. Everything else tested good. With the new TPS I have been able to get the idle to calm down a little. However, it sill has the hard start periodically. It is a strange issue, the majority of the time, it will start just fine. When it does decide to act up, it will pop and just sound horrible, but once it starts, it runs great.
As far as the EPS codes, yes they are only for that module. It stores its own codes separate from the ECM. I've read that the speed sensor will cause these issues as well, but it passes every test in the book perfectly. I'm going to do OHM tests on every wire in that part of the system and see of anything seems out of wack. Seems like it has to be a wiring issue maybe. The issue is so random though. It will do it on cold starts sometimes, but mostly after warmed up.
The throttle cable is adjusted with about 1/8" of free play as well. Diag reading on the TPS is between 15-20.
For some reason I still keep wanting to say valve adjustment, but I have already checked them twice. Unless my manual is giving me the wrong specs....
Battery is brand new, starter does not dragging or straining at all. When it has the issue, it sounds just like the timing would be off or valves would be out of adjustment. Sometimes backfiring in the exhaust.
I will update with any findings in the wiring system. If nothing is found there, I will have to think that it is the EPS issue causing everything. Which is not a good problem. The module is about $800. I wish I had a spare to plug in and try. I don't know anyone with the same bike anywhere near me.