Brutis

I had just finished a swap in my 2001 camaro from an ls1 (that threw a rod) to a ls6 out of a 2004 Z06 vette. It had a pretty big cam already in it, comp cam 235/242 115lsa +4. I had it tuned and the first problem we ran into was the passenger side bank was dumping fuel. The driver side was fine but the trim was not regulating the passenger bank. Narrowed it down to the valley plate had oozed sealant causing a gap in the intake. Seemed to fix the problem and he dyno tuned. Here is where I need an experienced tuner. We blew an 02 and replaced it. Fuel pump kept jumping around between 42 and 48 psi (I'm passing it off as the car was hot when he checked the pressure as it supposed to be cold, but we had pressure) I have stock exhaust heads with the AIR system still attached. He had me pull the vacuum line that runs from the backside of the manifold, comes up and over to the AIR sensor looped to the shutoff valve located on the driver side in the rear of the manifold. I understand if I had headers this would be eliminated but I'm new at ls1's and didn't ask questions. It ran great for a bit but when idling around 800rpm (I have a yank 3200 stall btw) the car would shake and start flashing the SES unless i kept it around 900 to 1000 rpm. Autozone scanned it and it pulled no codes. The first day out the gas was pretty decent but now it is sucking fuel and idling rougher then before. Any clue to how important the AIR system is and if the vacuum line being pulled would cause this problem like the vacuum leak did the first time?