LS1 intake on a 2004 5.3L

I'm helping a guy work on a C.O.E. and he has a LS1 intake on a 5.3 with the electronic pedal and TAC, hes running the truck MAF and the truck MAP. He is having a high idle issue. At start up, it idles at 1300-1500 and never idles down. I haven't done a scan on the engine yet. What I'm wondering is if the high idle is coming from the computer seeing the MAF and MAP table of the truck manifold? He has checked for vacuum leaks with fog, propane, and starting fluid and there is none. Also how would the proper PCV hose routing be with the LS1 manifold?
Thanks in advance.

The MAF/VE would want to be gone over again because the on the big difference in intake manifolds. Base running airflow and things like that will be different as well.

Ok, that's what I was kinda thinking. Just want to know I was on the right track before I drove two hours to try and tune the ECM. Wanted to rule out a hardware problem before
Thank you again for your help.