I think we figured it out. I took the boat to a buddy who is a mechanic first, instead of having to pay the local dealer $75 per hour to fix it.
Turns out that the raw water pump went bad and was spitting water on the alternator, making it short out the ignition/computer fuse. I know it sounds weird, but the alternator is working fine now. We hooked a hose up and ran it for a few minuits and everything works fine now. The dealer wanted $194 and said it would take 1-2 weeks, So I just ordered the pump from
www.i-netmarine.com for $117 shipped to my door in 3 to 5 days. This way I should be on the water by next weekend.