ECM problems

I have a 2000 flht that has been running poorly (to rich it think) burps and spits out the AC lots of carbon on the plugs,won't idle and the check engine light has been on for quite some time. I added a power commander that I mapped and still it runs the same w/ the engine light on. I just washed it after switching to the stock ECM to see if the engine light would go off. I started it up and let it idle for a couple minutes and then it died (like it always does when I touch the throttle) and wouldn't restart. I check for spark and had nothing. I pulled the ECM off and notice I forgot to put the dust boot on and there was some water accumulated around the ECM. I have tried drying it out but I still get no spark. I need help. Could I have fried the ECM????

I'm confused, why would you add a PC if you can't get the engine to run without spitting out the AC and the plugs fouling. That's a pretty expensive bandaid. If there is water in the ECM plug, blow it out and let it air dry for a few hours before plugging it back together. A coating of dielectric grease on the plug ends before mating it would also help with displacing water and keeping the plug from corroding. Fix the popping and fouling problems before you try to remap the EFI.