Dang, a very great post brother.
I have a warm spot for the first gen. KLR's, they are cool. I have a gen 2 (2009) though.
The exhaust header bolts being loose is rather common- I would not read much into it.
If you decide you might want to send the head out to be done, I know a guy in California I could suggest.
When you get this machine back together and you have verified it's running sweet, take the time to clean up the entire wire harness and look for abrasions. Wire and harness abrasions are very common and annoying on these bikes, but easily remedied. Nothing that about 20 feet of various diameters of wire split loom and hockey stick tape and zip ties won't cure. Also, even the little shitty wires behind the gauges can abraid from the vibration and leave you stranded...... wrap em in split loom! There are parts of the frame near the wire runs that are sharp as fillet knives !
While your handling the harness, unplug each connection, hit it with a blow nozzle, and dab a bit of dielectric grease into each connection before you bundle it up. Also, where the big master fuse is low on the frame, check that one out and clean up any green fur that may have grown in there, and hit that one with some compressed air and dielectric grease.
This will be a great post to follow, consider me subscribed.