Well thanks for all the input, after putting everything back together she seems to be doing ok. Rode her around for awhile earlier and things went good. shes been sitting for three hours, just check the battery, still at 12.9 volts ..thats a good thing. Gonna spin her around some more tonight. After riding for about 40 mins, the new connections to the reg/rec were barely hot at all. Screw them molex connectors lol. Will update on progress.. thank again guys!