Stand Alone 5.3 starts great.....Idles rough

Hi all, I am new to the forum, and new to the LS world. I am in the middle of setting up a 2004 5.3 for stand alone operation on an engine stand. The reason for this is, I work for a restoration shop and we are wanting to get in the LS swaps for our customers. I am setting up the stand so I can use it for multiple motors. I have the motor set up and the harness complete, tuning the motor with HP Tuners.

I have no experience with fuel injection or HP Tuners. When I say No experience, I mean I opened it for the 1st time to delete the VATS for this motor. The problem I am having is, I have the VATS disabled and everything hooked up. The motor fires up great and runs smooth for abut 2 minutes and then it starts idling rough. The o2s on HP Tuners seem not to be cycling the way think they should be. The LTB2 goes from 1 to lower 20s rather quickly, once the rough idle starts. I have checked for vacuum leaks as well as replaced the MAF sensor and tried running with it unplugged. Nothing seems to help. It sounds like its running on 6cyls. This motor is running on a stand and I made small collectors for the Manifolds. The collectors are about 6 inches long and o2 bungs welded in, but they are not hooked to a muffler yet. Am I missing something simple here in the tune, it definitely seems to be an air/fuel issue. The o2's were brand new. Any thoughts on where to head from here would be great. As soon as I find out how to insert the scan from the first start up, I will post it. Thanks

I apologize I forgot to mention the codes I was seeing that I was concerned with. I get a random Misfire (0300), MAF (0102). When I clear these and reset the PCM they come and go.

Have you done a compression test yet?

sounds like it's doing it when it enters closed loop......my first guess would be those collectors. How far from the end of the collector is the O2? Could be sucking some air up that collector enough to skew the AF on that side and it's dumping fuel. That's where I would start first. I'm assuming no leaks upstream of that O2 right? Either one of those will cause your symptoms.