Replace your voltage regulator, it is faulty.
I have also had this problem in the past, the unregulated voltage to your battery is overcharging it to the point of failure. I also explains the heat. A new regulator is an easy plug and play install.
Check your rotor. If you still have original rotor it is proned to failure where the magnets cone off due to the crap Yamaha design. I had a similar issue and it was the rotor. It may not be you issue but worth a check.