Rode it fifty miles today, tried matching RPMs, and that helped a lot. Early shifting seems preferred, probably because it is at lower RPMs. Checked the oil level afterwards, since a previous check showed oil higher than I remembered filling it, but the oil level was the same. I'll keep an eye on it for the next few hundred miles, but hopefully there isn't a head gasket or water pump leak.
New tires will come on Wednesday. I'm still bothered by the very tight caliper mount clearance on the front left and this is a good time to figure out a solution to get at least the (IIRC) 0.7mm of specified clearance. I was double-checking the parts diagram, and there's nothing missing or wrong. Front left and front right rotor are the same part number so they can't be reversed. Wheel only goes in one way due to the speedometer assembly. Axle is orientated correctly. My working hypothesis is that the axle nut was overtorqued at one time, causing it to ride farther in on the axle. Can anyone think of a reason why it would be a bad idea to throw a thin 15mm washer between the axle nut and the speedometer?
I'm also wondering if there's a gentle way to wash grease and grime off the engine without risking the 40 year old components. Any suggestions? I tried a brush and dish soap, then rinsing it off with a hose, but that only removed some of the grime. (I also temporarily killed the bike - three out of four of the spark plug recesses had clogged drain holes!) I'd like to get the engine clean enough to detect any possible leaks (so far, oil and coolant levels are not dropping).