[M_nation]

Alright guys, pleased to be a part of the forums. I've been a lurker for a while using other's posts to solve or diagnose problems, however today I have a problem that I cannot find a solution to.
I have a TaoTao Atm50-A1 with a gy6 engine.
Here in Florida we had bad rain for about 2 weeks without a break and I've continued to use the scooter. I imagine that's normally ok but there were also some deep puddles I've had to slowly wade through. The scooter still worked ok for a while. The blinkers hadn't been working for nearly the entire time that I had the scooter and I decided to finally get around and replace the relay. However the relay that I ordered caused the main fuse to blow as soon as I turned the key switch on. Well I figured out the cable colors weren't matching and switched the pins around and it worked great. Recently the scooter stopped sparking, so instead of hassling with diagnosing the problem I decided I'd just buy all new electrical parts ha-ha. Everything prior to this point happened within the 2 weeks of rain.
I replaced the stator, cdi, and regulator. Yay it works! However, when the bike revs it blows the main fuse. At first I thought maybe the blinker relay was still the culprit so I removed it but no luck. I've followed as many wires as I can to see if it's shorting but I've had no luck finding any. Could the rain have ruined something I'm not thinking of of? Or is it something else?

Thanks for all the support guys.