Hello John,
Well, I don't think that a 280SE / W108 with (4-speed) stick shift is particularily more valuable than a car with auto transmission. Most owners prefer the auto I think.
Furthermore, the overall condition (being rust-free, originality,options) decides how much a particular car is worth, not so much the auto versus manual question.
The 4-speed manual gear box is interchangable with the Pagoda gear box - if tunnel-shifted.
If column-shifted, then the gear box top lid would need to be exchanged.
As to the 5-speed, yes, I there was one available but only after 1969 (for the 108's with the wide tunnel). This is for sure not the rare ZF 5-speed that fits the narrow Pagoda tunnel but the also rare (and bulky) MB 5-speed with side-mounted levers, the MB G 76/27 (A)-5.
Not usable for a Pagoda if you had one...
Pic is somewhere from the WWW and belongs to that particular homepage owner.
Not mine.
Achim
(without 5-speed MB G 76/27 (A)-5)