so my bike was fine (turned over and started) but last night i charged my battery overnight and threw the battery in and now all i get is a click sound. its sounds like its coming from starter . ne help would be great

 

Sounds like the battery is dead, are you sure the charger was functioning properly?

The clicking sound is the first function of the starter when it is engaging the starter gear, but does not have enough power to turn the motor over.

 

i just got back from buying the new battery but i tried the old one first again. This time it worked and the bike ran. So is it really the battery or something else.

 

It would have been the battery, you may not have had to buy a new battery... But rather be sure the old one was charged.

If the new battery dies, there is a problem with the charging system on the bike (rectifier or stator)

 

also is it normal for the stator cover and the voltage rectifier / regulator to be hot

 

The stator cover is part of the engine, which gets quite hot... So due to thermal conductivity it will get warm.

The rectifier also gets hot like a normal electrical device (laptop, cell phone) and that is why they burn out... Aftermarket rectifiers are available with heat sync's for longer life.