What I am going to suggest might seem obvious, but it could be a lot of the problem. I suggest twisting the positive and negative voltage supply wires around each other. I remember the early fuel injection computers having issues with their injector drivers until they did that. Twisting the input signal wires around each other is a good idea, too. (5v signal + gnd). Twist all inputs and outputs if nessesary, but start with the heavy current users 1st.
I was putting together my Rostock MAX 3D printer 3yrs ago, and noticed in the forum that they have feedback issues, so I twisted all my wires in +/- pairs, and never had a problem. So from then on, I twist everything. ABS wheel speed sensors have twisted wires going to them as well, as they are touchy amplified inputs to begin with.
Worth a shot.
How about some PCM pinouts?
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