Beaureed

Hello everyone, I am looking for some help. I work for a restoration shop in MI. and we are just starting to get into the LS world. Fortunately I have been tasked to figure the wiring and PCMs out with these things. I currently purchased HP Tuners. So here goes. I am working with a 2004 DBW stock 5.3. It is set up on an engine run stand and plans are to get these running and be able to drop them in as we need. The only thing I have changed in the tune are removing Vats and rear o2s. It starts up great and runs great in closed loop, once it goes into open it starts with a real rough idle. I can turn it off and fire it right back up no problems there. It throws code P0300 and I can not get this thing figured out. I did the harness following LT1swap.com. So here is what I have tried with no success. I ran this in forced speed density and still seems to have the same rough idle

New Maf
New plugs and wires
New o2s
starter fluid for vacuum leaks
noid light on injectors cleaned and checked all injectors
fuel pressure is at 54-58 PSI

I'm stumped, I wouldn't think anything else in the tune would need to be changed. Any ideas out there. I have posted on Hp tuners as well, but I will post the tune file and scan file as well as some pictures of my setup to see if anything stands out to anybody. Thanks for any help I can get.