Upgrades
The electrical toys are largely transferable between cars, the only real issue being the changing of the electrical plugs used between mk3 & mk4 cars so you may have to replace some plugs with after market items. In my case, as part of the dashboard replacement detailed elsewhere on this site (link further down this page), I replace my entire mk3 loom with a mk4 version and fitted all of the available mk4 toys. As already mentioned, each of the additional equipment options requires its accompanying loom. I would suggest that you just fit all of it that you can get hold of, even if you don't have the working parts to go with it. At least then if you do manage to find the equipment you want to fit the wiring is already there for you.
As far as the bodyshell goes 'upgrades' are a subjective matter but here are some of the alterations I made to mine.