A headache

[Collin_Coffelt]

I will be very detailed here; I have a problem that is perplexing.
Changed lifters on a 2001 3.1. Two were making noise, but other than running a little rich due to repeated PO442 (small vacuum leaks), it ran fine. I have done this sort of job so many times before with no issues...
After getting to the point of pulling the intake manifold, I pulled the pushrods on one bank, one at a time, left to right (cyl 1,3,5). I wiped the top of each, carefully numbering them and laying them on a shop rag, in order.
I hand rolled the engine inspecting cam lobes. All was fine, very little wear.
Then, after swapping out the lifters, I replaced the pushrods with the numbered end up, spun the numbers around so I could see them and took a couple of minutes being certain was in the correct spot. I hand tightened, no ratchet, the rocker arm bolts. Then, I set my torque wrench to 89 #/in. I had a 30 degree template done on CAD (yes, overkill), and after each was tightened to spec, I went the 30 degrees more.
Then I did the 2-4-6 bank, the same exact fashion.
The new Felpro intake gaskets were installed: the nubs that go in the alignment holes on the head insure proper alignment. Silicone was used where the manifold meets the block.
I reinstalled the fuel rail/injector assembly with new o-rings on the injectors, again, Felpro. I did have to really reef to get the injectors out of the wells.
After reassembling everything, I rolled it without the module connected at all. She spun freely with no hesitation. That was a sign no pushrods were reversed.
I have verified all vacuum lines are intact and where they should be: I have a shop manual from GM
She backfires through the exhaust. When it does start, it is very lopey, catches and runs smoothly at 3000-3500 rpm, then lopes and repeats.
I have verified regular spark with an inductive timing light. The plugs were changed as it was close to the service interval. I ohmed the wires and they were within specs.
It acts like it IS vaccum, but the only place I can think of would be the new plenum to manifold gaskets, however the Felpros should not need silicone sealer as they have those built-in silicone gaskets.
I cannot see the module or the coil going bad from disassembly, or an injector (the rail was pulled using those four pads on the intake manifold), but I suppose it is possible.
If I unplug the MAF, the engine immediately starts and runs at 3000-3500 rpm then choppily steps down every few seconds(might be telling me something there).
My next options are
1) Spray water where the manifold contacts the heads,
2) Get water down in the injector wells to test the new o-rings,
3) Ohm out the cam and crank sensor,
4) Swap out the MAF for a known good one.
5) Ohm the coils,
6) Take the module and have it tested.
Any other thoughts of something I am missing?
Maybe an O2 sensor? Going to go pull the MAF and see abt cleaning.....