I would think you have pulled threads or stretched cap bolts to go along with that big scrape... threads look ok in the pic but it's hard to tell.... will they take full torque (104 inch pounds)? replace the bolts, Helicoil the threads as required was the piston divot on the right side? that would explain why only one valve hit & not both
Looks like spring parts took a free ride to the top and bounced all around getting under the decomp, I'd try the valve cover on and torque the bolt, if it holds don't worry about the scrapes..doesn't really matter. Pretty sure 104 in lbs is way too much, 55 in lbs for the valve cover bolts that go into the cam caps and 69 in lbs for the other two. When you split the cases you want to pay special attention to the needle bearings on the ends of the shafts, you can see one in the pic I posted. When debris goes between the gears it will spread the shafts apart and the needle bearing is the weak link. Fiddle around with them, spin, wiggle..if any needles fall out they're bad. I would be replacing every bearing in the entire engine plus the oil pump, there are a couple of bearings in blind holes that are hard to get out, a welder helps or take it to a machine/engine shop.
... let me rephrase that. the holes for the bolts that hold the cover look fine (and ya, 50- 60 inch is right, depends on your source) the ones you are worried about are the ones that hold the caps on the cam journals.... those are 104 in/lb and I meant left side for the divot (left when sitting on the bike). what I think may have happened is the spring going through the chain cocked the gear & shaft so it hit the side or the head.... the only way that could happen (I think) is the cam cap bolts either stretched or the threads got pulled. so again.... replace the bolts & helicoil as required. and if the divot is on the right side Larryboy may be right & the spring went through the decomp lever (trying to figure how only one valve gets hit) but pretty sure thats not what put the chunks in the case & piston.... something else. in fact mebby a couple and btw... the cam chain should probably go in the dumper too
Marknet says the rotor puller tool is a 22 x 1.5 mm bolt. You might be able to find one locally instead of buying a puller. But the Motion Pro tool is less than $10. http://www.klr650.marknet.us/Doohickey.pdf Don't forget to buy a replacement bolt for the rotor. It's a one-time-use bolt.
The decomp only cracks open that one valve under normal conditions and at low rpm starting speed it doesn't hit the piston...crack that valve open at idle or higher and it will tap the piston. It only took a few seconds to carve out the gouges we can see and that's when the valve met piston.
So I've been insanely busy with work. Also, not a single place within 50 miles of me sells anything 22X1.5 as far as I can tell. I refrained from ordering a puller online because I wanted to get on it right away. Would've totally arrived by now. Bottom end should be apart Tuesday. Anyway, I figured I'd educate myself on what the hell goes on with valves. Had a hell of a time getting the shim bucket out on the one in question. I figured what you guys have been telling me: bent valve - maybe pinning the bucket against its' "sleeve." Finally got the bucket out by spinning/pulling. Pulled the valve, but it looks pretty normal (compared to others, google image searches for 'bent valve') and slides with absolutely no problem. In an ideal situation, I'd send this thing out to some adv reputable head guru who would make it sparkle, but I still have the unlikely prospect in my mind of getting it going by 6/7. I'm actually ok with pulling it apart later and sending it out as long as it doesn't explode on this trip. As far as I can tell the only problem (which may be fairly serious/I have no fix for) is that the shim bucket won't slide very well on the valve in question. There is no visible scoring or anything on the outside of the bucket or inside of the sleeve thing. the bucket appears to still be round (I know, tiny differences) so I'm not too sure where to look. I know they're not supposed to be swapped, but I tested it in the other sleeves and it slides no problem. I assume the correct answer is port and polish? I still await what lies at the bottom of that engine...
I have a 2011 KLR 650 that locks up almost every time when down shifting from 5th to 4th. You have to be very aggressive on the downshift and if your real lucky it may go into 4th. Most of the time it hangs up so you have to upshift back into 5th then really shove it back down. I've replaced the clutch pack and clutch cable so far. I ordered new shift rod, pawl, spring clip and shift rod spring. They will be here Monday. If these don't fix it then I'm getting rid of it. I've put 1000 miles on it since I bought it. It's been down more than it's been on the road.
That won't fix it, you have a bent shift fork on the drum, split the cases to fix it. The only way a shift fork gets bent is by the operator. May as well sell it now.