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I have my system setup similar to yours, and what I usually wind up doing is reinstalling all the programs into the same directory so that the registry entries get put in. It MAY be possible to install it for the registry settings and then overwrite the dir with what you previoulsy had installed to get back your old settings.
Generally with windows, reinstalling the program is the only way to save it. If you save the registry and then reimport it it might work, but odds are that there are tons of files installed into c: drive even if you wanted the whole program installed to a different drive.
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