have you tried taking it to a pro-tuner? I doubt anyone will have a base map for such an odd swap. Whoever supplied the wiring should supply a base map as well with all configurations set already.
Tuning is what I do day in/day out.. I just don't mess with many domestic motors so I am working with pretty limited information.
The trigger configuration is definitely the problem, I am just asking for assistance in determining the crank/cam trigger wheel setup so I can input it correctly. What I have been finding is that it "should" be the same as the neon, which doesn't work for this vehicle.