Hi Alan,
Just yesterday I was mooching through my BS Bookmarks and rediscovered Ray Oliver's web site,
http://bridgestonemotorcyclerestoration.com/ and learned a couple of things that I hadn't read before but relate to your questions. Look through the 'Service Letters', particularly the 5th one down, BSG-0000, Continuous Customer satisfaction, Issued in July 68. It sheds new light (to me) on the issues you refer to.
Crank Shaft Seals Although BS have stated the engines will run quite happily without the crank end seals, they still thought they were worth retaining and redesigned the crank recesses after 21F05701 'to permit positive seal retention'. So there's your answer, leave them out before 5701, unless you can improve the retention as Z's reply, and refit them after 5701.
Crankcase Sealing It seems BS originally used dilute sealer on one side of the cases only and leakage was known to occur, usually by the front right engine mount in my experience. After 21E05455 they used full strength sealer applied to both sides of the cases. This maybe explains why, on a later engine I've just stripped which had never been apart, there was excess sealant all round the case joints including the gear box seals.
I don't think the gear box can be out of sync, just make sure you can shift through all the gears and that there is clearance on the change dogs when in neutral, before bolting up , maybe do a dry run first.
Hope that helps, Brian. P.S. There's nothing sad about a 50p BS lapel badge (Great buy), I've still got one from 45 years ago !!