Motorcycle Repair: air cooled bikes, piston rings, noise issues

Question
when riding one day. It was a hot day and iI was riding my XR 350 honda. i had been riding for the past 3 hours and decided to head back home. how ever I was caught in a thunder storm, thus causing pudles on the sand roads. I then hit a puddle as they were unavoidable. All of a sudden two loud "clicking" noises came from the engine. I think it could be the piston rings that could broke or some thing in the engine head compartment that could've cracked. If im not mistaken the bike year is a 1989 or a 1987 model. The guy who owned it before me was the head of Linex Yamaha South Africa and if im not mistaken I think he might of changed the pistons and tried to make it faster. If he did do that then could it have been possible that the bike could've had to be run in again?  

Answer
Hi Kyle.
 Did the bike run after the the "clicking" noises?  If it did, the clicking noises continue?  If they continued, did they change speed with the engine?

If the bike continued running and is able to be started normally, then nothing in the head is broken.  Worst that it could be, would be a busted rod, but you would have noticed a very noticable drop in power as well.

If the bike still runs normally (without the clicking), then it could be something else altogether.

The problem with diagnosing engine noise issues, is that almost any noise could be almost anything.  Have a local mechanic look at it if you are having issues with the bike.  Something like that can only be diagnosed properly in person.

Sorry that I can't help you more.

Good luck and ride safe.
FALCON