Bottom, working up.
1. Depending on which version of Vista you have, it being your OS won't be a problem.
2. FFX, all the files it needs are installed in their individual folders. The latest version is FFX 3.3 for FFvTTR. Uninstalling the main game will not affect FFX. As for FFvTTR, the game will not erase any of your saved games, meshes, or extra content unless you check the option for it to do so when you uninstall.
3. Digital Jester installations provide their own set of problem in regards to mods and extra content, but I don't know if they ever attempted to clean that up. For your sake, I hope they did.
4. My suggestion would be to do a full clean install (outside of extra content) and build on top of that. I'd make an effort to keep the latest version of FFX you have safe as the MAIN site to download that add-on is down and may not be back up anytime soon.