I suppose I should update this. The bike has been running very well. The general feel is like that of a new bike, which is what I wanted. With a couple of suspension adjustments, the steering is near perfect. I slid the forks up through the triple clamps a few millimeters and took about half a turn of preload out of the shock, that's it. The steering is neutral and practically effortless, but stable. It is hard to imagine a better-steering street bike than a stock FZR400 ... but it is. About the only criticism for street riding is that the ride is pretty harsh. At some point I may swap out the 20-weight fork oil for 10-weight.
1000 km since rebuild (break-in for new piston rings) passed last Thursday, at which point I changed the oil filter and put in Amsoil 10w40 synthetic oil. There was nothing scary on either the magnetic drain plug or in the oil that was drained out. Oil consumption appears to be nil.
Earlier in this thread I mentioned that I had raised the needles in the carburetors by one clip position to solve a cold-engine driveability issue. That was too much. Fuel consumption increased (was around 4.5 L/100 km, now it's low 5's) and I'm told the exhaust smells rich when riding, and today's ride in warmer weather revealed some rich chugging down at the bottom of the rev range. So, tonight's chore was to put the clips on the needles back where they were but with the washer underneath the clip, which basically puts it halfway between where it was last year, and where it's been this year up until now. Haven't ridden it yet with this adjustment. Having the airbox off also allowed confirming that there is no longer a coolant leak at the thermostat housing.
The cylinder head work - smaller intake ports - greatly improved mid-range (above 4000 rpm - below that is where it feels too rich). It's now actually possible to overtake cars without downshifting three times. It's no ZX10R, but it does actually accelerate below 10,000 rpm.
Keeping an eye on the battery water level is a chore that I don't miss ...
There is still a to-do list, but it's all minor (and will likely wait until next winter).
Something that I completely forgot about last year is that both backlighting bulbs in the speedo are burned out. Can't see the speedo at night. The bulbs are probably $2. Taking apart the upper fairing completely in order to get to those bulbs ... can wait.
There is something machined slightly out of tolerance in the spacer between the front wheel bearings. If you clamp up the axle, the bearings go tight. For now, it's put together without the axle tightened (so that the bearings are not preloaded) but locked in place with the pinch bolt; it's not going anywhere so it's not really an issue. Fixing this requires disassembling the front wheel due to the captive spacers. That can wait, too. The way it is now will work, it just requires not following standard procedure for installing a front wheel.
And, I don't like the cush-drives that these (and most other) aftermarket wheels use. They are FAR too hard, and provide negligible cushioning. I can't help but think that this contributed to the transmission failure that I had with my race bike last year. I have concocted my own cush-drive bushings out of a steel washer and a combination of 4 rubber O-rings in each of the 6 drive pins, in place of the very hard urethane donuts that the wheels shipped with. This provides roughly the same cushioning (going by feel) as the stock cush-drive in the stock rear wheel, BUT, those O-rings don't last. (Fortunately, they're cheap.) What's really needed is to fabricate new urethane bushings that are roughly 70 shore A in hardness (much softer than what the wheels shipped with), but that's likely also a winter project.