The hi-res REX clouds look great on my system, but with anything more than sparse clouds the frame rates drop to low single digits.   I went back to REX and selected the 512x512 textures and "use DXT", after a minute of loading it said done.  But back in the sim nothing had changed.  I know it's the cloud textures since, in spot view, I can pan around til no clouds are visible and the fps returns to normal (locked at 24).

I'd try manually copying the files but not sure which ones, or to where, or if renaming is necessary.  Permissions aren't an issue since FS9 is installed on a separate partition from Vista.