Car is running on 5 cyl's, can anyone figure out why?? LONG

Alright guys, this is my friends 88 GT.

Heres the story,

He bought my old gt40x heads and B cam, we put them in, he also got a new typhoon intake, 24# injectors, and got his pro-m recalibrated to the 24#er's. He did the lower intake byhimself and didnt seal it to the block well. We noticed it once we got the car running cause it was leaking oil out the back and front. For that ONE night it was running it was running REAL strong, real fast, idling perfect, everything! I was very surprised after all the issues my comp gave me with the B cam. Too good to true of course,can never do some good sized mods without a headache with these cars.

So, he went ahead by himself, and yanked the lower intake to reseal it. He left the gaskest on the heads, as they were in great shape still. After he buttoned it all up, the car will not run right! It sounds like a damn lawn mower. He determined that its running on 5 cyl's. The primaries off these cyl's are not getting hot. I believe its 4 5 and 7. We confirmed that THERE IS spark at all these wire ends, and that the fuel injectors are shooting fuel.

Ok, heres what we have tried thus far, and we are getting very annoyed witht his car.

- tested every wire end for spark
- Changed the plugs a bunch of times
- Got a new cap and rotor
- got a new coil
- got a new tfi module
- Set it to top dead center multiple times to confirm it was right.
- Moved other injectors to the same spot as the dead cyl's - still nothing
- Removed the fuel rails and turned the engine over to confirm there is fuel spitting out.
- Did a compression test on these cyl's, #'s were good
- Pulled the VC's off to look for a broken spring or pushrod, nothing.

While the car is running, we could unplug the injectors or plug wires to those 3 cyls' and the idle would NOT change.

So WTF is going on here, there IS fuel going in, there IS spark, there IS compression, WTF is left to be wrong!?!? Leak down test?? Im totally out of ideas here, im not a good trouble shooter to begin with, and this stuff just pisses me off. Hes picking up a code scanner from his work..

If we pull the plugs to those cyl's out, they are covered in fuel. So yes, we would think theres no spark, but there is!

Any help at all on what to try next guys? Hes loosing interest in this car fast.

Thanks guys, i know someone will have an idea

Thanks for the responses!

We tried everything you guys mentioned. We hooked up the plugs to the end of the wire, and grounded it out, nice blue spark.

I know its weird, but there is fuel on the plugs when we pull them out. We have tried changing the plugs many times, the gap is at .40 now, still nothing.

I was not there when he did the compression test, he said they only did those 3 cyls' We will do them all again to douible check since its easy to do anyways.

We also tried putting a diff set of wires on those 3 dead cyls.

Heres a question for you guys though, TDC is when both valves are closed and the piston is all the way up correct? Will the car run if its not at TDC?

The wires are correct on the dist.

Im completely stumped with this car.