LS1 spits,sputters,backfires,fouls plugs

I would seem to think since you changed the intake manifold, it may not have seated properly when you installed it. It sounds like you have vacuum and intake issues. You may want to re-check your work, make sure head gaskets are seated properly and the front and rear seals. Re-torque intake bolts to the proper ft/lbs. Torque the bolts on the intake starting from the middle and working your way out.

well il do that, but just sent the injectors off to be cleaned, thinking it could be that, so if that was my issue why would it run fine once it warms up?

was doing research and found out I have 2 fuel pressure regulators 1 on fuel filter by gas tank, and one on injector rails don't know if that would over flow the fuel or not?

It's always tricky to tune an engine that is not original equipment. Just out of curiosity, what did you use for the engine control module? Did you pull the module out of the Silverado?

yes, but got it tuned to removed vats,delete egr, delete air pump, eliminate skip shift, and the different injectors and ran it with a painless harness, not so painless now lol