Basically the only drawback is you trusting someone who wrote the script for the Car or Mod...If they knew what they were doing it should be easy as pie. If they didn't then it could crash your game...but it can be fixed by simply uninstalling it...VCMM makes a backup for what ever car you choose to overwrite..
I'm pretty sure you can get the 996 ( there is also a GSXR1k, R1, various other relatively old bikes around on the net..)
Here is a .VCM for the 996, After you DL it, unzip it, and read the instruction file.
Also for "most" .vcm files you will need the Dmagic's Wheel Mod or something like that...Vice City Mod Manager can install that for you..It's already in it, when you install VCMM..
Please make backups of everything, most importantly these files..
and gta3.img(it's named that even though it's Vice City)
again if you have anymore questions just post em...
I have been doing this since GTA:3 came out for PC
I have Vice City installed and have NO original cars that came with the game..
And once you get "used" to modding the txt files, you can add or create your own custom colors to use for cars..