Sounds aren't what they seem...
2008 KLR 650 purchased from 2nd owner, 3 mos ago with 10,500 miles. Doohickey and some other mods done by P.O.
I’ve put another 2,000 miles on it and feel like I've been diligent about the maintenance. I got it all dialed in for a 9 day trip into 60% highway, 40% dirt trip into NV, ID, UT.
A week before the ride, I noticed a very faint grumbling noise from the front end, only when moving at low speeds. Much slower than crank or cam speed, it sounded like a speedometer head bearing, but the speedo was operating fine, no bouncing needle etc. The noise wasn’t audible from either side of the bike - only above the forks, behind the fairing. Clutch in, clutch out, not much different, but only when moving. I pulled the front wheel and checked the bearings and they were fine, so I assumed it was my speedo head and I proceeded to prepare for the trip.

Day 1 of the trip, cruising through Zion National Park, after about 300 miles of pavement (subtle noises being difficult to hear in those conditions), the noise was back but its character had evolved in a worrisome way. Still pretty quiet, but now sounding more like a grind at low speeds with torque applied. Again, nothing audible on either side of the bike, only behind fairing, only when moving. Now I’m wondering; balancer chain grinding on case with torque applied? Counter-shaft bearing? I traded bikes with my buddy (also a Gen 2 KLR guy) but he didn’t hear anything. Neither of us wanted to end the trip, so I decided to keep an ear on it - hoped I’d be able to pinpoint and correct before heading too far into the back-country.

Day 2 Next morning (with bike cold) I adjusted the doohickey and for another few hundred miles, I was unable to reproduce the noise.
Looking for camp near Elko, NV (Jiggs), riding slower now, the noise was audible again. Still wanting to continue on this epic ride, I reasoned that maybe the Doo didn’t get all the adjustment it needed today…I’d adjust and check again tomorrow.

Day 3 Again, with bike cold, went through the Doo adjustment procedure, but leaving camp, the noise was even worse. I couldn’t ignore this any longer, and with sub-freezing temps and a few days of precip in the Jarbidge, NV forecast, I told my buddy I would not be riding into the back-country until I got this figured out. We limped the bike into Elko and pondered the situation over coffee & breakfast. By this time, I was picturing something really sinister going on and realized I needed to rent a truck and head for home. Riding to the U-Haul location, my buddy was finally able to hear the noises from where he was sitting on his bike. With earplugs.
Loaded bike and drove 12 hours home, while my buddy continued the ride solo.

I worked the rest of the week to try to re-coup some of the expenses.
Saturday morning, I intended to pull the left side cover off, but investigated a bit with my mechanic’s stethoscope (Harbor Freight, dirt cheap, but a long screwdriver does the same thing). On center stand with front brake locked, safety strap, fired it up and took a listen.
Nothing abnormal from engine case.
Put it in gear and the noise was audible but not as bad since there was no load. The engine case sounded normal, but when I listened to the case near the front sprocket I thought I had pretty good confirmation of a rotten counter-shaft bearing. Engine off, turning the rear wheel by hand, I could feel it binding occasionally. But having my hands on it brought my attention to the chain and sprockets. (D’oh! Really?!) I thought they were pretty good before the trip, but now I noticed a few tight links and some stretch. Rear wheel off, in neutral, the front sprocket turns smoothly. New chain and sprocket set coming this week and I’ll know for sure if that was the problem, but I’m 90% certain it was.

Why the noise presented from behind the fairing, and not from the left side is a bit of a mystery, but I have a theory: The cupped shape of the skid plate channeled the noise up in front of the radiator, past the steering head…?

Anyway, I’ve learned lots from this. I’ve always done my own work, and I’m a pretty good parts replacer, but it turns out I need some development as a troubleshooter. And while I’m embarrassed and disappointed that I ended the trip early and spend a buttload of $ on a truck to get home, I have to look at the possibility that maybe I’m sitting here right now precisely *because* I ended the trip early.

Don't beat yourself up too bad over it. It really could have gone either way and had you gone on proved to be even more expensive. It's only now that you are at home that you have the resources to check everything a little more thoroughly. You win some, you loose some. It's only money. See how it sounds with a new chain. Did you measure the old one?
I had a similar experience on a trip once myself. Heard a noise but couldn't narrrow it down. Finally noticed the chain had way to much slack, tightened it and all was good. Except I had to adjust it pretty well everyday after that till I got home and replaced it.

Sounds to me like you made a good decision to stop when you did and secondly that the repair was much easier and less expensive than it could have been. All in all, Good Stuff!

My original chain made a noise when going up through the gears. It looked good, and sprockets were like new. Even service mgr. at my local Kawasaki dealer said the chain was Ok and adjusted properly.
I took a chance and put a new chain on, and no more noise.

Chain, sprockets, prevailing torque nut and chain breaker coming tomorrow eve - will measure Thursday then and get back to ya guys.