Yea did you lower the attitude PIDs? I had to go way down on my 200mm with 1306 motors . With defaults they got very hot, very quickly (in seconds). That may account for your voltage issues too.
And BTW, log a flight and check the VIN values to get an idea of what is going on with onboard voltage (and everything else). We can't really tell what is going on w/out a log either.
-Max