A really quick thing to check is whether Zidane has a Mage Masher already equipped, that's an early way to know how things are going. Generally speaking starting a brand new save file is probably a good bet, otherwise your inventory might have some things in it that it really ought not to.
However since my last post there's actually been a number of big changes and it's actually pretty easy to set up the mod with Moguri now, if you want to give that a shot. Just have to do the following:
1. Install the latest version of Moguri, the download link is as follows:
https://www.moddb.com/downloads/mirror/216757/127/bfacb6ef7e75fa89cd9b57b3d09a2a232. Download and run the latest version of the Memoria patcher from this page:
https://github.com/Albeoris/Memoria/releases. Note that when you run the patcher, Windows may pop up a dialog saying the file is unsafe; this appears to be a false positive and is probably not unexpected given how the patcher works.
3. Launch FF9. You should now see a different looking screen from what you would normally get with Moguri, what you'll want to click is the "Install Mods" button in the upper right-hand corner. From there, click the Browse Catalog tab and you should see the mod listed. Not everything listed is current available for direct download through the manager, but from what I can tell that will change soon.
4. Install David Bowie Edition and go back to the Installed Mods tab. From here you may need to alter the load order; so long as David Bowie Edition is listed above the Moguri files it should work just fine.
MASSIVE thanks to Tirlititi for getting this all figured out, none of this would be possible otherwise.
Even if you don't want to run Moguri for whatever reason, I'd still recommend doing everything here after the first step. Memoria is generally superior to the original engine at this point and it makes installing supported mods like this one way, waaaay easier.
I should note that there might be bugs, I've been testing it myself and had some other folks do the same and there have been some oddities here and there, most prominent one at the moment is that the area around Dali seems to occasionally lock up during random battles, but it's fairly easy to get to Dali with minimal battles and it's not guaranteed to happen to you. Once I've had an opportunity to test the fix for that I'll update this thread and the file within Memoria; from there it'll just be a simple matter of uninstalling and reinstalling the mod.
Last thing I'll say is that there will probably be a number of balance tweaks forthcoming (I'm not super into how the start of the game plays in retrospect), but otherwise everything should be playable and stable.