I also think it's electrical and said as much in my first post in this thread but we will see what he comes up with once he's gone through all the trouble shooting on the electrical/electronics side of things...what was the part # for the internal harness you replaced?
unless you have the wrong separator plate and/or gaskets using a pwm pump and 96+ valve body should work in your 94 case. I don't believe you can use a pwm pump with a non-pwm valve body. this sounds like an electrical issue to me
EDIT: did you use manual valve out of the 94 or 96 valve body?
@tuffy331 - Manual valve differences (93-94 on the left)
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