I wouldn't worry about valve seats or circlips. The later trannies have other mods that I think are a big improvement. The valve seats sometimes last as long as any. Heads with 40mm carbs have monster big ports. I think they are border line too big and not the best shape.
Smoothness? Even my dad liked the R80 for it's smoothness. Personally, the main thing I notice about them is the lack of power versus a R100. They have always reminded me of a R90 that way. Why not go bigger than 94mm bores? Personally, I think BMW stopped at 94mm for a lot of very good reasons. I think BMW thought they went too far at 94mm. I think they took it as far as it makes sense to go.