[twowheelertoy]

How long have you owned the bike ?
Whats the mileage ?
Serviced regular ?
Always done it / Just started / Gradually got worse over time ???
Does it back fire at all either on cranking or running ?

There are a number of things that can cause your grief..

Ignition timing out. (CDI faulty)
Water getting into the combustion chamber.
Mixtures incorrect.
Air leaking into the combustion chamber.
Carb internals loose/siezed/worn.
Valve clearances.
Faulty battery. (Sounds daft but you'd be supprised what problems they can give you)

 

[twowheelertoy]

Ok.
Only numbers 2 and 3 getting overly hot would just about discount the CDI.

I would do a compression test to illiminate the valves.
Then have the carbs apart and clean out thoroughly and set the mixtures and balance.
Battery as you say will be ok.

Good luck..