Honestly I think most of it was bad turbo. Went through reeds, tps, fuel pressure, dobeck box, wiring, clutching, chaincase, probabaly forgetting some things other things i checked, went through a lot of stuff. One big no-no that Corey found was the oil pump being plugged into the ECM power plug instead of the DC power plug (right next to it) due to worn labels on the wires. While it is obviously good to run it correctly from the DC power plug, it did not make it run any better. Adjusting the tps idle helped slightly but not enough to make much difference. At the end of the day, my thought is that the turbo was going bad and not spinning freely at idle, causing too much backpressure and making it not want to idle. This finally became apparent when the turbo actually bit the bullet and obviously needed replaced.
Before putting on the new turbo i threw on the stock muffler just to see if the old turbo had anything to do with it. Sure enough, with the stock muffler it suddenly idled just fine. Put the new turbo on and it idles correctly now. (and runs better too)