I basically went through a similar problem, and I threw parts at it from friends until I basically narrowed my problem down to wiring harness or injectors, here is the thread from my ordeal last year (sled is running great this year as well as at the end of last season once I got it going):
http://www.snowest.com/forum/showthread.php?t=392726&highlight=860
I did stator, full engine compartment harness, ECU / ECM, capacitors (2 including the one in the harness), fuel pump, several fuel filters, direct voltage to fuel pump, pressure tested fuel system, stator and flywheel (stator supplies current directly for the injectors through the ECM)... buying a complete used fuel injector harness (off ebay) with injectors attached of the right color (and for an 800) got my sled up and running again, I still suspect it was the big connector into the ECU / ECM but no way to know for sure, I kept the "bad" harness and injectors for spares since they could be replaced one at a time if necessary.
So no guarantee it is the same problem, if you have a buddy who will switch parts with you off of his sled to test them that is helpful, otherwise it might be a little pricey trial and error (you can buy used off ebay like I did for some of them but there is always a chance the part you bought has an issue and that plays mind games with you). The last thing I changed that fixed it for me was the injector harness with injectors, I ended up putting everything else back and giving the loaner parts back. Cost me quite a bit of time out of my season to troubleshoot... if you were close I would loan you some of my spare parts to test everything out with...