Those pics sure take me back

I dug up this old thread for ya :http://forums.sohc4.net/index.php?topic=38903.0
Tim in Ohio logged his entire 350F build very well here and it's a good read. Some of the questions you have are probably answered in there already. The 350F engine is very similar to the 400F and the fundamentals are the same.
I also had a broken cam chain adjuster lock bolt in my case, and I had to get a machinist to repair it. Luckily he's a friend of mine

. He said it was a difficult job, and I recommend you do the same. The problem is to properly drill out the old bolt, it has to be rigged up in a mill or something. Otherwise it makes a mess to do it freehand.
As for the wear on the U shaped adjuster....It's junk. I got one through Westernhillshondayamaha.com....but I hear they may be running low on those parts...they're a common problem on these wee fours.
Two of the cyl. head studs are a different length; the two near the inner cylinder spark plugs. All the others are the same height.
You've done well so far, It took me a lot longer than you to get mine torn down like that...good work.
Matt.