Diagnose this engine knock...
 

Been riding the rebuilt engine for about 2000 miles now. The bike is a '92 XT600 E with a 96mm wiseco piston installed.

While riding the other day on a fully warmed up bike, I stopped a total of 2 times and each time I went to restart the bike knocked once as it fired up. Just a single knock. This has never happened to me before so I was surprised when it happened. Hasn't happened again since those two times.

Could it be the fuel? Running too lean maybe? I am riding with stock jets in the carburetor and at elevation of 5000+ ft., basically in the mountains is where most of my riding is so I thought i'd be running a bit rich, actually.

Other than that, the bike's been running great!

Did it sound sort of hollow, like a sharp knock on a wooden door?

Yeah, that's pretty much what it sounded like.

No idea; mine was doing that at about 6000 miles. 10000 miles later it's still fine. I asked around back then and no one seemed to know. I've actually even heard my dad's XR650L do it before.

I'd guess that it could be something to do with the piston position at firing. Maybe when you crank it over, when it's at that specific position, the ignition timing doesn't have a chance to get, well, timed and causes a nice, heavy detonation.

Maybe it's when the piston stops near the top of the compression stroke, so when you fire the engine the next time it still fires, but the piston literally isn't moving fast enough to compensate for the timing, causing the engine to knock when the piston "slowly" moves through the compression stroke.

Does it happen when you use the electric start?
Some XTs Clonk when switched off I think this is the starter clutch, does not seem to be a problem.