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What exactly are you doing? I use the megasquirt wiring harness, known as a db37 harness, to connect all necessary wiring to the MS ecu. Check it here, not my thread but way more organized than me!
zerothread/164446
If that doesn't help, I would move on to a different approach, he did it the easy way. I have been working on getting a nissan CAS to work and read off MS2E for a while now so I can make the megasquirt more nissan parts only. Using EDIS can get old, I have had road debri move the vr sensor before and cause me to have 10* of timing all the time, that was a b****. I will have a machined sensor bracket from now on.