Thanks all for the advice. I got my problem sorted!
Took my bike to Corsa Meccanica here in Toronto, and they checked the entire charging system. Turns out the short fried my older battery (5yrs). It was showing charged, but would not do much with the bike. A quick check of the regulator, new battery install and the bike is running great.
The wife and I took a trip to Manitoulin Island this past weekend and my bike ran great. Her Suzuki TU250 as well.
George and the team at Corsa are great and helped me in a pinch