So you've mentioned Tool RF a few times now and I figured it was some late game thing. I never got it on any of my GFs. It's still an ability, right?
These were all of my abilities at the end.
GF Levels:
Shiva 60
Ifrit 45
Carbuncle 45
Bahamut 58
Cactuar 51
Tonberry 51
As for PuPu, yeah, I went to Winhill Bluffs and tried for a few minutes, got attacked like 10+ times by monsters and no PuPu. Then went to Timber Beach and again no PuPu, just a lot of random encounters. I can try again if you want.
And I'd definitely be very interested in your 1v1 idea or any other alterations you make to Seifer. I have a save right before the final boss fight with him.
As for stat/level progress, I made a video of me defeating Seifer 2 where I start by showcasing levels and stats:
https://youtu.be/M348_Z2xLy8I have saves right before Seifer 3, Ultima Weapon and the final boss if you need levels and stat reports from there. Unfortunately I saved over all my disk 1 saves after a while.
As for how to improve stuff, damage seems the big one. The tank thing at the Missile Base was really easy compared to most mods I've played. NORG was also a pushover. Maybe those were intentional nerfs on your part, though.
And I guess it's a good thing I saved all of Selphie's Ultimas for the final form of Ulty. I only managed to draw 15 from Ultima Weapon but it was still more than enough to destroy Ultimecia in no time. Made it the easiest part of the fight, honestly. I'm not complaining - Ultima should be King, as you noted earlier. It just made me very happy to do like 13K damage a turn with just her and her Double.