Strange Rattle??

Just been recomissioning a GP200 and have fitted new gearbox bearings, chain, tensioner and kickstart shaft. I also took the top end off and fitted a new small end bearing and gaskets and whilst I had it apart I cleaned up some light marks on the piston and inside the barrel and cleaned up the cylinder head then lapped them both. When I got it running I noticed a bit of a rattle on tickover and immediately thought it was something to do with the gearbox/chain. Took the side case of and nothing obvious so adjusted the bottom chain guide a little just to make sure the chain wasn't hitting it and checked the chain tension which seemed good. So don't think the rattle is related to that side of things but seems to be coming from the cylinder/flywheel side. Doesn't seem as though it's the flywheel on the cowling and have checked to make sure the head cowling isn't touching the exhaust downpipe or anything obvious like that. The scooter starts fine and ticks over and seems to run ok but when it's ticking over I can still hear this strange rattle? Nothing sounds loose anywhere either. Anyone got any suggestions on where to start, could it be I've over done it with the tidying of the barrel and piston and am getting piston slap or something like that? I only cleaned the marks very lightly and they where still visible when I reassembled? 
