This topic might be on the irritating side for those who know what they're doing when looking at a .gba file (i.e. everyone except me, apparently), so just bear with me as I am in need of assistance

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OK, so very recently (like, yesterday) I decided to try the FF4 Advance GBA version of the game and see if I liked it. It's a bit on the slow side as far as battles/graphics, but I haven't gotten anywhere near the extra parts of the game that are new (such as the Lunar Ruins), so I guess I'll keep going...more to the point of the thread, I decided I wanted to transfer some of my old ROM edits over to this particular incarnation. Now, I wasn't surprised to learn that .smc and .gba have some differences by any means (this is the first time I've ever looked at a .gba file), but I thought at least there'd be a similar 'indexing scheme,' such that, say, the Job Command and Spell Learning lists in the .gba are in the same or at least a similar order to the ones in the .smc file.
No. No soup for me. I finally find the stupid Job Command list on my own, after discovering that, yes, the order the commands are stored in the ROM had changed (along with almost everything else, right down to how many bytes were involved with each separate field of the level-up data (this went up from five to
sixteen), and apparently trying to find the character's names is a no-go).
So Rydia is '00 04 07 08 02' rather than '00 02 03 04 01.' OK, I guess that's not a problem...wait, where's all of the space after the command lists? This section of the data flows straight into another set of values that I have no identity for (certainly not the copious quantities of 'FF' that usually succeeded these things).
Also, the two sections of the ROM in the .smc that used to control which magic menu went to which character for the purpose of learning spells (FFFFFF|FFFFFF|020304|0506FF|FFFFFF|etc.); no idea where they are for the .gba file, tried looking for them using different arrangements of menu values (I don't even know if it's 3 bytes/char anymore or not).
I've gleaned a fair amount of information about other aspects of the .gba file from datacrystal.org and romhacking.net, but these particular parts are being annoyingly elusive; also, the 'Spells Learned by Leveling Up' data is likewise completely sandwiched in by 'relevant' values, and not the big filler space I was used to.
I'm beginning to think the only way to work around this is to find whatever points to that location in the ROM and redirect that to somewhere way near the end of the file, and just rewrite it from scratch. At least .gba files are easy to expand so you can actually relocate blocks of data, but I haven't ever had to find where the game stores whatever it is that points to the start of the 'spells learned' table before (so I...kinda don't know where to start :/). Is this making a mountain out of a molehill/is there some much easier way to edit the commands so people aren't stuck with 3 or 4 instead of 5? Should I just stick with the SNES versions (which I've had no problems editing)?