I've noticed the loss of performance too while editing gp4. That was the main reason why i've built my proggy. No more re-installs of gp4 for me..
Now my gp4 stays 100% intact, and i can play with all the graphics i want.
BUT a 'slow' carset with large graphics will always stay slow, can't change that (yet
).
And about 3Dmark... well said!
I know people who buy a new graphics card just to gain some extra frames in 3DMark :S I just think they are pathetic.
Its a waste of money, and like you said; it doesn't guaranty an increment of performance.
About your 'problem'.... (don't know if it is a problem)
Leave both installs on your HD and use 1 of them as a 'trashcan'.
Update cars etc.. and keep the ones you want to keep, and store them in a new cars.wad, and do the same with other wad files. Place them in some folders on your HD and 'switch' the original and the new cars.wad whenever you like. You can patch the exe file with any program and this won't affect your in-game performance. Just keep an old backup of the exe in case anything goes wrong.
If you have downloaded carset which have an install, you can try to install them to a tempoary folder e.g "c:\temp\" after that just get the cars.wad, anim.wad and the performance files etc.. and do the other stuff by hand.
Maybe you already know this, but maybe it helps someone else who is reading this long boring post of me