So I took my bike out to the dunes yesterday and everything was running really good, bike felt great, but when I was stopped on a dune idling the bike while waiting for my buddy, I heard a fairly loud engine knock. I heard it before when I started up the bike, but I didn't think it was a big deal because when I replaced the oil seals, I noticed my clutch basket fingers were work down a bit. I ended up just filing them down so the plates wouldn't get hung up and I'm aware that this usually cause a slight rattle. But that sound has been bothering me. Could it be piston slap? I just re-did the top end last summer, so things shouldn't be worn out. Compression is still good, it's still a pain to kick (high compression head).

The other possibility is maybe the wrist pin bearing...? I don't have the thrust washers in (weren't there when I took the bike apart, didn't know they were a thing) I was thinking maybe crank bearings, but I checked them when I had the bike apart and they seemed fine. Is a knocking sound associated with a bad wrist pin bearing?

Like I said, the bike ran good and I'm loathe to get the top end completely re-done since I'm on my last bore with this sleeve.

Any thoughts would be appreciated.

I was on fb tild about slap thrust washer. I didnt have thrustwasher on both my first topends and they lasted 18monthe between the 2. They started of quite and where they didnt have the washers it just beated the piston up. First one knocked the pins out for ring gap to lay on. Second one broke pins out again and busted squurt and junk out above the rings.  If they are not in their your running a time bomb. You coule tear it down and measure. You might be able to get by with a hone and new piston. Also rm 250 99 wrist pin bearing and billet thrust washers. Which are in forum store.

Even if you find out it's the clutch, like LT250RWV said, you are running a ticking time bomb by not running with thrust washers in. I upgraded my stock ones last week with the billet ones and the RM bearing from Mitch. Mostly because I had a blown head gasket and had to tear down anyways. $45 for the washers and bearing is cheaper than a rebuild and I prefer the peace of mind over wondering when the bomb is going to go off.

I installed all that stuff. Bike still took a **** today at the dunes. I guess my luck just sucks.

Luck has something to do with it, jetting might help abit more. I know that's what I needed to work on!

A good indicator of a sheared woodruff key is that it will in fact have spark, but with no way to control the timing, it will pop & back fire out the intake & exhaust. And if you catch it just right, will kick back on the kicker & damn near break your foot.
I'm here in Yuma as well. Hit me up & I would be more than willing to come over & give you a hand with it.