Thanks for posting, it is heartening to watch your progress! I am about 2 steps behind you with my own 2002 640Adv, thought I'd start a project while I am between jobs waiting for the first child to be born (any day now...)
I am sure you would not miss this given the extent of your work so far, but have a good look at the carb. I have pulled mine apart using the fantastic BST-40 bible on the site. It was dirty as hell, all plastic parts were shot and my needle was down to 30% of the original diameter:
That was a near miss! I can +1 for the water pump shaft seal, if you go anywhere near the head it is a must do.
And some headlight protection; my Touratech Spectacles were in mint condition after 10,000km. They broke in a fall, I rode 80km further and now I am up for a new headlight. And it had to be the more expensive low beam one that blocked the stone
Look forward to watching your progress