Sounds like you rode her hard, and put her away wet. I love my Bestop Mesh Bikini, as if you drive above 25, nothing gets wet. Battery connections ok? I would take her out in the sun, open the hood, spray WD40 over the whole motor, start it up, and after warm up, close hood, take her out for a short spin. Water got in something, but could just be a ground issue arising. Were you driving in this downpour you speak of? or parked, then drove?
2008 Red Rock Rubicon Unltd 6spd dual top