Hmm...from your response toe #2 above, another thought:
have you tried to rotate one of the front forks in the triple trees, to see if one of them (or both?) might be slightly bent? If they were run into something hard in the past one day, they would be ever-so-slightly bent backward, and this is hard to detect. I test for it by turning just one of them in its loosened clamps to see if it rotates 360 degrees without binding the fork lower's travel. If it does bind, they might be slightly bent. This isn't terrible, so long as the bend is adjusted either straight forward or backward on both forks: the forks will still work OK - they just need to be 'paired' in their arcs for that to happen.
Reason I ask: once in a pit crash (1972, involved a bikini and a long-haired 18-year-old brunette in the pits), a Suzuki (X-6 Hustler) slightly bent its forks. All was fine until 85+ MPH when it started wobbling a bit a few races later: they had "discovered" the wheels were not in line and offset the rear wheel to make them so during between-race maintenance. The real issue was that they had rotated one of the front [bent] forks with front brake work, which then offset the front wheel a bit. Realigning the front forks together, and with the slight bend backward on both legs together, returned the handling to normal (if they did lose a few mm of trail in the process). That was one fast little twin!
Her name was Barbara, if it matters...