EFI regulated Water/Meth problems

Hey everyone, i have a snow Stage 3 water/meth kit with digital controler installed and tapped into the Fuel harness to regulate based off of injection pulse. When the car runs for a few minutes the controller starts to read spikes in injector pulse and the system begins to spray like crazy. (Luckily nozzle not installed). The car idles and drives fine and my wideband dosnt detect the fuel my digital controller reads is dumping. My question is what could cuase this besides a faulty controller. I have an upgradded 255 fuel pump without a relay mod and wonder if that could be affecting it and potentially endangering my ecu. I also changed my fuel harness back from batch fire. Other then that i am stumped on this 1. I supose i could just run boost reffrence but its not as accurate or efficent. Any suggestions would be appreciated.