Thanks for time replies.

Hitting the sack now. But will reply proper in the morning.

Regarding the noises I've heard. The "clunk" under the seat I believe to be coming from the starter itself. When I pressed the starter, I heard the noise and (as I'm still holding the starter button in) nothing else happened. It didn't continue to try and turn over the engine. Just nothing. Then second press and all was fine.

Regarding the "ping" noise, I could almost believe it was a rock on the first one. Though I swear I "felt" the vibration in my foot when it happened. But the second time I was at the side of the road at full stop.

I'm going to take it for a good ride tomorrow and try to record the sound of the clunk. Recording audio is my job. I'll bring my portable recording setup with me. :)

This probably has nothing to do with anything, but I haven't been able to shift smoothly consistently since the gearing change. (13/42) I figured I needed to get used to shifting at a higher rpm. It's like shifting at anything under 6k and it wants to "jump" into gear. But not always. Maybe this is normal?

Sounds like your clutch is hanging up. I would check the adj on the clutch to make sure pulling the lever fully disengages your engine.
My bike definitely makes the same clunk sound. And still does after replacing the bearing on the clutch idle shaft. It was doing the same thing last ride. Hit the button, clunk and locks up, next time the starter works.
I am thinking there is something out of wacko in this system on my bike that causes the clunk. I used to think it was the ACR, but don't think so now.
The starter has a clutch in it that engauges only one direction. I think the engine is kicking back while the starter clutch is engauged and the starter will not turn backwards, the thrust is then released on that idle bearing. Since I never tore that part of the system down for inspection, I don't know anything about it.

I am hoping my new bearing will last a few thousand miles, then I am going back in and checking it. I want to replace it again before it ruins the cases, otherwise it is just a nuisance.

Thanks for your input. I think I've read about your cam tensioner on advrider's klx250 thread. That's you, right?

Your tensioner is on my list of things to buy. Figured it would be several thousand miles down the road before needing it though.

I'm going to drain the oil real soon. As good a time as any to open things up to have a peek.

Silly question...assuming I don't accidentally destroy them, I don't need to replace any gaskets when putting it back together, right?

Make sure your chain is not too tight. That might have some effect on shifting. Just a thought. Better slightly loose than too tight.

Not sure what your gasket questions are about. If it is the oil change, the O-ring on the cover and the soft aluminum one on the drain are reuseable. If it is about the tensioner, I send two gaskets with the kit since it is a custom cut gasket, the stock unit has an O-ring.

I should mention, I would occasionally get starter noise if my 650 kind of kicked back when it shut off. As said, I think it was part of the starter drive set up since it has some sort of one way clutch set up on it. The tensioner makes a noise usually when it is failing, up around 4000-6000 rpm range unless it's really bad. It isn't catastrophic when it goes bad, you have time to deal with it when you notice the noise, part of the reason why I don't say fix it now, don't fix what ain't broke. And listen where noises come from. It is amazing how you can track noises fairly accurately.

I wanted to follow up on this. I went for a two day ride last week. Loaded her up real good and pushed her hard. Everything went smooth as butter. Not a hicup.

The only thing different was an oil and filter change. Before the problems started, I started using Fuchs Silkolene Comp 4 10W40. I had read some guys saying their bike can be finnicky with certain oils. So decided to try something different/cheaper this time: Shell Advance Ultra 10W40.

Seems a long shot, but any possibility these problems were simply "oil related"?

Auto decomp will make some noise(clank/clunk) when a failure to start happens or a stall at lower RPMs

I used to think this, but no more. Specifically what do you think is making the noise? The ACR does not seem to have any parts that would slam appart or back together.

If you are using a synthetic, why not take advantage of the longer life. On dyno oil I run 3000-5000 miles without concern - have for the past 45,000 miles on the 650 and still going.

With synthetic I wouldn't hesitate to 5000-8000. Heck, Mobil1 first came out advertising 15,000 mile intervals. They only quit doing so because they felt the claim was hurting sales since there is a firmly entrenched myth that changing at 2500 or so is best. I'd think the oil company knows more than "Bob's grandpa". We're dealing with 21st century petroleum/synthetic oil technology, not 1950s straight weight non-detergent stuff.

I guess what I'm saying is if the oil works use it, just extend the interval about half again or even double the change interval mileage.

If you do want to "cheap out" why not go to Shell Rotella, either dyno or synthetic, since both are JASO-MA rated - they meet wet clutch motorcycle engine needs.

The auto decomp has a couple parts the 'slam' together; ACR acting on valve bucket, ACR resetting, valve opening/closing out of time. I'd pop off the valve cover and have a look at least, check your valve lash while your in there.