Yeah, it's rather unlikely that you'll find a patch that only changes the battles. They aren't at all the most obviously broken part of FFT, and most people will do things like make Archers usable or turn Calculators into Red or Blue Mages.
If you do opt to set it up yourself, you're probably also best suited to manually giving these guys custom secondary skillsets rather than just choosing the generic secondaries. Special secondary skillsets are auto-mastered last I checked, whereas using the generic ones will only let them use what they've learned automatically based on their job progression. I have no idea if you'd still have those secondaries equipped upon Inviting them, though, come to think of it...
Also, monsters can be hard. They just aren't designed to be in FFT. As an example, Jot5 gives them small, but powerful skillsets, as well as innate skills. I'd take a good look at what the monsters in Jot5 can do and consider beefing up the monster skillsets comparably.
There are certainly more changes to Jot5 that help bring monsters up to the level of actual threats, but that's the most profound part of it.
If you do opt to set it up yourself, you're probably also best suited to manually giving these guys custom secondary skillsets rather than just choosing the generic secondaries. Special secondary skillsets are auto-mastered last I checked, whereas using the generic ones will only let them use what they've learned automatically based on their job progression. I have no idea if you'd still have those secondaries equipped upon Inviting them, though, come to think of it...
Also, monsters can be hard. They just aren't designed to be in FFT. As an example, Jot5 gives them small, but powerful skillsets, as well as innate skills. I'd take a good look at what the monsters in Jot5 can do and consider beefing up the monster skillsets comparably.
There are certainly more changes to Jot5 that help bring monsters up to the level of actual threats, but that's the most profound part of it.