This is a well written post and is reflective of another old school way of getting a mod to work. It works EXCEPT there are known issues with sound and multiplayer that are yet to be worked out as a result of the 10Gig "patch" and the devs at Steam are working on it. Which means yet more patches to come while they sort it out.
Honestly, it might be worth it to simply wait to do anything until the chips fall where they will as you might have to do it all over again.
I honestly couldn't detect any sound issues in custom battles or in the vanilla or Britannia campaigns, but I've barely tested it thus far. The only way would be to bug test it exclusively.
A check of the registry after doing a completely new reinstallation after doing a complete forced uninstall of the registry prior, shows the identical registry entries, and so it's possible that mods will still install and that save games MIGHT work if you carefully do as I suggested and migrate data for safe keeping.
The patch is 10gigs, and a completely new installation is 14.6 gigs. Honestly that mammoth a patch is bound to fail.
Example: there are reports that SS 6.4 has sound issues where the Americas' campaign music plays instead of the regular SS mod music.
Note that there is a patch of some sort that was supposed to fix the sound/MP issues on another forum, but the same issues remain. It will take a cadre of lots of players to hunt down these issues by trying different things within mods. I seriously doubt there will be any simple answers.
See:
http://forums.totalwar.com/showthrea...-Update-Hotfix