Had to create an account just to congratulate you on your efforts, clean job, and overall documentation of the whole journey, forums are a dying concept so it's nice to see new posts with current acitivities, properly described and with images, I'm sure a lot of people stand to benefit from your log of this rebuild on this website, make sure to share the scrambler progress too!
I have an er-5 from 2001 as well, been my daily commuter ever since I had a license, and it is my dream to pull out the engine some day to give it a proper service, at the very least lap the valves, clean thoroughly and paint it completely, but we know it's never as simple as we plan it to be hehe there's always dicoveries to be made and new parts to be ordered.
At this point she's in the garage waiting the end of winter, I have my coolant tubes are leaking so I have to remove, clean, and install new O-rings on those f**kers, will take the opportunity to open the valve cover and gap the valves, then the spring time carb clean & fluids, and it should be ready for this season, that and of course, replace the rear tire and balance the new one, I tried to remove the old tire manually on a vice but the second bead doesn't want to break away, went to bed on Sunday evening with a pulled muscle on my forearm and extremely frustrated lol