The issue with a standalone on the LT5 is the shear number of outputs required to drive everything. I haven?t researched the MS3, but driving 16 injectors plus 8 individual coils, plus a 4-wire stepper, plus ..... there are a lot of outputs needed. You?re not likely to be able to do all of that with a budget ecu. Waste spark helps (reduces 4 outputs). You could conceivably run the injectors in parallel, and fire PRI and sec at the same time. Buts that?s a bigger current draw on the drivers. Inputs are never the limiting factor in my experience. You need to add up all the things (outputs) you need to control and find an ecu that has that capacity. There aren?t many.
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