I'd like the option to specify source and destination (for lack of a better word) ... search for duplicates of those files in folder A where they are found ion B,C, or D .... BUT not between the latter (I.E. between B and C).

This allows for quick checks without having to re-do the entire thing.

If you can't find it .... reinstall again on top of the current one and then look for the uninstall

Just remember that there are two types of folders here ... system ones like MY MUSIC, DOCUMENTS, etc. and folders u created.
U can move folders as you wish (more or less) but pointers from other programs or the OS itself , in the case of system folders, have to be modified.
There are programs to tell the system where the system folders are located. Your programs will have to reviewed usually under OPTIONS/PREFENCES to make sure they point to the new locations.

Remeber ... we are talking data folders here not program file folders... I strongly recommend keeping program file folders in place because of the registry entries.

See this for free partition managers http://www.techsupportalert.com/content/best-free-partition-manager.htm