When you reinstall the program, I would indeed go for the default location for your game folders, including saved games, in My Documents. That is where the developers intended but you must make sure of the location when installing the game. Look carefully at the location when it asks for you to confirm it.
I think your saved games (.lg folders) can just be copied over from the x86 folder to My Documents. Any skin mods that you did can be reproduced; just do the same things that you did before and delete skin.bin.
What people usually forget are modifications that they made and/or saved, like custom database files, templates, logos, uniforms, etc. Copy and paste.
One other thing; when you UNINSTALL, I think the game asks if you want to delete certain things like saved games, etc. You want to say NO to this, do the above, and only then manually delete what you don't want anymore.
Sorry that I can't be anymore explicit right now; I'm at work.
