Yes, that's pretty much what I have found out and explained. On the -98 FE 400 the flywheel nut is 15mm and in a hole, so normal ring spanner won't do. The marks on the fly wheel and crank case are these in the picture, I assume. Similar marks for the ignition and TDC. I'm away from the bike until next week, but yes, I'll do the valves again after closing the cover and this time properly when valves closed AND the cam-decomp not interfering (keeping the exhaust open). Btw I have a new favorite tool and I can measure the valve clearances fairly easily with a help of that: a small metal pike / "hook" that turns 90 degrees in the end. With that I can get the feeler gauge to right way.
Still need to find out how to do the ignition timing, but I think there's info about that around. And need that strobe and a puller.
Still need to find out how to do the ignition timing, but I think there's info about that around. And need that strobe and a puller.