Has anyone tried using the same custom SFX for both games? I mean, install EZFX and FFX to each game as usual, but when you add your own FX, just add them to one texture and generic folder and use FFEdit to have each game look for the additional FX in the exact same folder.
I'm gonna try it on a couple of FX, but I'm wondering if anyone has already tried this, and if there are any problems in doing it. It would save some small amount of hard drive space if it's possible.
The only problem that may come into play is the FX native to both games being cross referenced. FFv3R might be fine, but FF1 could wind up calling FFv3R fx, which may have unintended secondary effects.
Other than that, if you take steps to set up everything carefully, I think you should be fine.