This should be straighforward, except that I believe you are going from an externally regulated alternator on the 85 to an internally regulated one with say, the 3g unit. You would have to remove the external regulator and the wiring that goes to it. The indash amp gage probably won't work, but I have never seen mine move.
There may be some clearancing needed to get the newer unit in the bracket also.
The original alternator in an 85 should be at least a 60 amp unit, and you should be able to get an 80 or 100 amp direct fit replacement. From the mods you listed, only the electric waterpump would seem to be an excessive draw for a 60 amp unit, otherwise it should charge the battery just fine.