Go for a ride until you start to feel the warmth, then stop, turn off the bike, remove the seat and feel the battery carefully. If the battery is getting so hot that it's literally cooking you, something is very very wrong with the wiring. Considering your rectifier fried (not common), it sounds like there's a short, a switched polarity...something going on.
Have you added any electrical mods to the bike?
It could simply be a bad battery.
If the battery is literally HOT, get that thing checked out ASAFP - you do not want your battery cooking/melting etc. while you ride.
Any other electrical probs.? Rough startup?