Broken Stopper Lever and gear noise, 2006 YZ450F

So the other day i was out taking my boy for a ride up the canyon near my house and my bike started making some bad noises. Sounded like chain/gear grinding, almost like grinding gears when you miss a shift in your manual transmission car. Called my wife to come and pick us up. The bike has been very difficult to shift for the last month, should have remember the stopper lever issue with these 06's, but that bearing had come apart, and I have retrieved 7 of the bearings, and both cages. The outer race was still in place and showed no sign of damage.

My next question is, what has everyone been doing when this happens? How much damage can those little balls cause and do i need to tear the whole engine apart to be safe? Also can anyone think of a situation where those balls could cause a grinding sound from my motor? I have ordered the new 07 stopper lever and will install it, but still don't know what to do with the mysterious noise. Everything in the motor looks good, all gears in the primary side as well as the cams/valve bucket area, as well as the magneto counterweight.

Any ideas from anyone??

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