Long winded rambling skippy!
I'm with the others of the opinion that if you take the time to pull it down you might as well give it the full treatment. Its very little extra in 'work' to replace everything, and honestly the bulk of the time is spent cleaning and removing things down to the stage where you actually remove the internals.
With the trans, take lots of photos and references to how it all goes together. Turning the counter shaft gentle you should be able to put the bike through its gears even with the set only sitting in half an engine case. Again, even more easily once the cases are together but not yet torqued up.
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