Think so but I will not know for sure until I get it back on the Dyno.
I have the Jimstim "for the MS3 Board" and JimstimX "for the MS3X Card" which will let you set up and check all the inputs and outputs on the bench. EVERYTHING bench tests fine so I know it is not the MS3 or the MS3X Card.
I have a message into a Megasquirt Guru/Tuner to go over everything. I should be talking to him tomorrow. I will be sending him my MSQ files and see what he says. He has been tuning and building Megasquirts for 10+ years!! Member fenderman33 got me his contact information. Thanks!