Hi all, I'm on the fine tuning section of fixing this Yamaha YBR 125 now and finally took her for a wee spin but the engine is making a horrible clunking sound. Any ideas on what this could be? 

could be fecked

You need to be more precise when you say "horrible clunking noise" cos that could just be your lunch box in the pannier.

Nah. If his lunch box was stuck in the pannier i bet there would be a high pitched scream..

Flywheel loose ?  whats been touched ,?  [ off]   and not tightened,

PMSLLLLLLLL to Cynic!

125 - Are you sure you have oil in it? Sounds terminal to me Either small end or big end???????

It's coming from the air box every time she breathes shall we say! Kinda sounds like a couple of dice, clunking around in there, It sounds like "cluh cluh cluh cluh cluh cluh cluh cluh"

When I was a very young man we had a woman turn up at the garage complaining about her car making a "strange noise", up on the ramp we couldn't see anything wrong so next round the front under the bonnet and still nothing obvious, lady took my mechanic out for a test run to demonstrate the "noise" he came back with the biggest smile! Seems that if your child leaves a marble in the ash tray it makes a "strange noise" The point of this story is that if it sounds like something loose in the air box then it's pretty certain that that's the place to check first, take it off and look inside to see if in fact you do have something rattling around in there.

Had something similar with a GSXR750. Really annoying tocking sound. Turned out the previous owner had put a conker in the air box to ward off nesting spiders!