Update:
Bled the front brake and pumped a container of fresh brake fluid through the master cylinder and caliper. Seems to work okay pushing the bike around the garage, but I expect at least new seals might be in order.
Changed the oil, replaced the primary oil filter, and cleaned the secondary oil fillter. I'll change the oil again at 100 miles to check for weird stuff. Oil is cheap.
Torqued all head bolts to spec.
Adjusted the timing chain.
Adjusted valves. This was a bit confusing as Yamaha, Clymer and the internet all have conflicting information about proper valve lash. I went with 0.003" intake and 0.006" exhaust, but that's tighter than the 0.006" intake and 0.008" exhaust spec listed in the Yamaha XS2 manual. Would appreciate comments on this from someone knowledge about the XS2.
Checked compression: 150psi left and right (cold).
Set points gaps and adjusted points to achieve proper static timing. Discovered the advance mechanism arms have a tendency to stick open so cleaned and oiled those - - - but they still stick a bit.
Started the bike and verified dynamic timing is okay.
The right exhaust is smoking a little. Hopefully just sticking rings that will free up. I'll try some Sea Foam and see how it goes.
Replaced missing rear brake switch.
Went over the whole bike front to rear to check for loose fasteners.