Wow... You wrote a long, long, LONG request. lol.
I actually have a full-time job with Siemens now (very good company). My time is basically non-existent. This does seem interesting but you may want to tag someone else for this. I'm always cool with helping out but the time commitments for this sort of thing are just too great. Also, I'm not as much of a brony as I used to be. Heck, I live three city blocks from the Double Tree hotel next to SeaTac Airport and I doubt I'll make it to Everfree 2017.
I've also never played the Golbez hack and I've only played through FFIV a few times and the most recent time was at least 5-6 years ago.
I was actually working with someone on the All-stars hack. Maybe you should divvy out responsibilities to ease your overall work-load on this project. It can also be tough to do that as quality often suffers (as it did in the case of my helper--I had to go through and "fix" all his animations).
I would recommend retooling all the scenario mechanics and then altering the sprites, music, and other things to make the game seem pony-ish.
Back when I had thought of doing this, I wanted it to take place during the Hearth's Warming era of Equestria. It seemed apropos to the to the setting of FFIV and would fit in the overall narrative. Food for thought.
Again, my workdays including the commute are about 11 hours. And then I like to hit up the gym and/or basically relax in the evenings. I also have other projects I'd like to get to. I have a student loan I need to pay off which might lead me to switch to a part-time job though that is still months from now. I'm also getting a bit too old for this sort of thing (lol I mean I can't spend much more time on "free" projects).
It is all interesting, of course.
You may have to do this if you want to see it done.