If the crankshaft was pressed apart and a new or used rod installed, there could have been a balance issue with the crank assembly. Also, the flyweights must align perfectly, or the entire crankshaft assembly will want to swing out of center, which can tear up the case.
We'll see what you find, Forman. Also, keep moving parts balance in mind when doing the reassembly. You don't want another 100 mile ride to serve as the engine's lifespan. Matched parts or subletting a balance job on the crankshaft assembly would be worthwhile.
I thought more about your cylinder head work. If the casting is damaged and there is severe valve seat recession, most single cylinder motorcycles get a new head. Honda castings are in the $300-$400 range, you're creative with used parts, and it sounds like there are plenty of KLR pieces out there.
This discussion is bringing back a flood of memories. When I worked construction and as a heavy equipment operator and repairs in the early 'seventies, I "followed my passion" on the side and opened an independent motorcycle repair shop. Though my forte was British motorcycles, I magnanimously worked on anything that came through the door, a good business move for a small town.
The Chrome Horse was a fun and challenging venture. Alongside BSA, Triumph, Norton and other British marques, this was the era of vertical shock dirt bikes, two- and four-stroke, plus the hot street two-strokes like the Kawasaki HI and H2, two totally lethal motorcycles good for nothing but straight line drag racing. Honda had revolutionized the industry with the CB four-cylinder engines. I was "in my element" as we say!
I worked on OHC Honda engines of the day and was always fascinated with the Japanese ability to machine precisely—regardless of casting appearances. The capper for me was mating two used and foreign case halves for a Honda CB350 without a bit of oil seepage or any measurable misalignment. Says much for Honda, though the appearance of frame welds were another story at the time. In fairness, they did hold.
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This was my life before four kids (now a bunch of grandkids, too), a fancy college degree from the University of Oregon and decades of chasing the brass ring (American Dream, take your pick of euphemisms!). The Chrome Horse at Carson City was my independent motorcycle side business while working construction and running heavy equipment at northern Nevada in the early to mid-'seventies. Motorcycles have been in my life for a half century now, my first operator's license was at age 14, a Nevada Scooter License.
Funny how some passions stick around! Donna and I have been married for 37 years.