Unfortunately if Ross doesnt know and no one else on the forum has replied, then you might be SOL on it. I have only read an E40 before and never got around to tuning it, plus it was a stock truck and not a swap. Swaps are tricky in this regard, just because the harness and ECM are setup correctly doesnt mean one other tiny thing isnt off. So you get fuel pressure, just no spark when cranking? To me that sounds like a VATS problem...but then again I might be wrong.
In addition to disabling VATS, you also need to apply the Disable VATS Patch in the OS then full flash the ECM. I dont know if your tuner did that or not, E40/38/67/etc need this done as well as changing the VATS type plus turning the VATS off, its not like the LS1 where you just turn it off and flash it.