I hate to be the rain parade guy, but your root problem, if you went with someone who does not have the background knowledge on the Viper application to get the job sorted. This is obvious, or you never would have ended up with a Paxton Fuel/Tuning system. Absolutely yester-year garbage technology loaded with issues, and not in the least the proper way to build it. With current technology, you should be running replacement rails/injectors, 2-Bar, proper tuning and pump upgrades to get you in the ballpark. Will function 100% as intended, on and off throttle. Not just a dart, dartboard, and hopes. DO NOT JUST WILLY NILLY BUY SHIT. Talk to someone who knows WTF they are doing, and buy it all from them.
I may have done this just a few times. Just because you can "make it work" in other ways, does not mean its friggen right. I dont do things the wrong way... I leave that to the other yahoos trying to make a buck.