sound like a train when accelerating
 

I have had this noise for quite a while now. The bike ( GZ 250 ) is now 16 years old, I have just renewed the cylinder and piston, valve springs etc and clutch. I was hoping that this would clear it up, the noise is not there on de acceleration, the engine is running sweet. Any help would be appreciated. The noise seems to be coming from the crankcase, or the drive chain and is accompanied with a slight jerking motion,any help ?

Sounds like you may be due for a new chain and sprockets. Give them a good inspection. If they look worn and you don't know how many miles are on them you may need to replace them. Pics would help us help you.

...or a worn out rubber inside the rear wheel.

Thank's. Water warrior, free wheeled down to my mates yesterday and still had the noise and chug a chug sensation, think you may be right, will send pic's and inspect. Also thank's 5th Bike. Have replaced all components in the rear wheel,as I also suspected that.