The rules regarding the surcharge to travel in a higher cabin for individual sectors specify booking in the higher fare class. The rules also state how the surcharge is to be accounted for in the fare calculation. If adding the surcharge when booking it will be included with the original booking; if adding it later it seems to me that it will require that the ticket be reissued as it is a change to ticketed points and the higher class may result in higher taxes and other surcharges.

I don't see why you wouldn't receive miles and credits for the class flown as you are paying for this higher class -- it is not a promotional upgrade. I don't believe it gets much discussion here because the surcharge is only available on certain airlines and the rates for the surcharge aren't really that good of a deal. If one is going to pay the surcharge to fly in a higher class depending upon which surcharge is purchased it may be time to consider just purchasing a DONEX. The rules generally don't discuss the earning of miles and credits that would be for the program you are crediting to.