Migration is not limited to once per save. On DPPt it's limited to once every 24 hours. Time starts counting after all Pokemon were caught from the Pal Park. If you change the game cart or modify the date on your console you have to wait another 24 hours.
On HGSS there isn't any limitation.
The met data is all wrong, Manaphy can not be bred or caught. Just get it from the encounter database (Tools > Data), don't try to create it from scratch.
Until transfering is officially possible through Home transfering through PKHeX won't be possible as well. Wait until Home gets updated in a few months.
Double-click on the box tab will open an additional box view window. Now you can drag them from the one window into the other without having to save the files.
What happened to this save? Did you use any cheats? Did you try to play it on an Emerald cart?
Your save has strange data at places where Ruby/Sapphire would never write to.
It might be possible to fix this. However save block 1 is gone. That's where your party and items are stored.
I haven't tried but I think I could restore your save with a copy of the block from another save. Do you have any older backup of your save?
Also to prevent future issues you should check your Supercard settings and see if you can get the save size set to 128KB.
Edit:
This is the best I could restore from your save by using block 1 from a new save: firered.sav
Nothing wrong, that's a new feature of mGBA that adds RTC data to the end of the file.
Use the dev build until the next stable release.
For compatibility with other emulators you can use an hex editor to remove the last 16 bytes of your file.
Those are your ROMs, they only contain the game data not save data. You should find your saves as .srm files in the saves folder inside your Retroarch directory.