Weak injector pulse, problems with ECU

[seen4ever]

Ok, background first:

ECU was originally on a stage 4b system over a year ago. I bought the ecu off a friend and pulled it off the car myself when it was running. I planned to put it on my car but my car has been down for over a year now with the engine build up. Well the time has come to get the car up and running. During the time I upgraded to the S200 and I have used my blue box to tune around 3 cars in the area, so I know that works properly.

We initially plug up the ecu with hondata, and check for spark, we have spark, next we take a noob light and test for injector pulse, there is none. This confuses me, but then I remember that since the ecu has just had a new chip put in, I never remembered to cut the jumper J12. So i cut both ends of jumper J12, made sure the hondata box had a solid red light and then we resume checking the noob light. This time we have a very weak injector pulse.

We had a stock p72 ecu sitting around, threw it in and it has a perfectly bright injector pulse.

My question, is this normal for the injector pulse to be weakened? We've tried starting the car, but it sounds like its running on 2 cylinders, so we turn it off in like 30 seconds. Now jsut about everything is new on the car, so we can start testing things, but the weak injector pulse has me thinking my ecu jsut somehow decided to crap out on me. Any feedback is welcomed.