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knocking i cant find

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Hello guys i have a 2002 rm125 and my brother was riding it at the track on saturday and it starting making a knocking sound like the the rod bearing went out so we packed it up and when i got it home i pulled the motor and to look what ill need on the rebuild 

i checked compression and it great 160 then i pulled head off and the crank and rod are tight no play at all... odd the piston looks great it only has maybe 5-7 hours on it from a new top end. 

so i pulled each side cover off to see if anything was loose i could not find anything i spun the crank and it spins amazing no rough spots in the bearings at all look at  the flywheel and clutch bearing waterpump bearing it all looks good only thing i could find is the gear that drives the water pump makes a rattling sound when you shake it idk if its supposed to do that idk im no stanger to motors i do it for a living but this has me stumped without just replacing parts just to hunt it down any advice would be great thanks 

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Is it actually a knocking sound in the engine? It could be jetting related I have 2000 RM 250 and after a rebuild if you crack the throttle right when its decelerating it sounds like metal on metal but its really just fuel igniting in the exhaust.. The increase in compression after the rebuild and break in may warrant a jet change or simple adjustment of air fuel screw or needle clip.

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And yes the gear that sits on the water pump shaft will be a little looser fitting than the rest of the parts under the right side case.

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It's most likely the crank/rod bearing, but you need to pull the cylinder to check that.

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