I had done a swap a few years back and had a similar problem. Turned out to be problem with voltage to injector power source. Power source needs to be a constant 11.7 or higher. Preferably 12.4 volts or they will shut down. Cause was a small gauge power source wire that would reduce running voltage down under 12.4 when motor/ECM was on. Cure was increasing wire to 12g and giving it a direct fused connection to a clean battery source. Also used a noid light to check injector wire operation and made sure fuel pressure remained at required 58psi during running.
Keep in mind this is assuming your VATS is actually removed. Good luck.
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