Making bosses change sprite mid battle?

You need to have the 2 monsters in the same formation, and have one hidden and one shown, then one of the monsters in the battlescript will have the trigger to hide itself and bring in the other one, depending on a timer or a variable. Look at formation #456 in usme and see how they have both the monsters there and one is hidden, then look at the battlescripts again to see how to go about it.

And you remove the magitek armor via event editing. Grab a copy of the event text: http://www.angelfire.com/al2/imzogelmo/s...Disasm.zip
and you would want to look for something like this:


CC/9948: 44 Place character $00 (Actor in stot 0) on vehicle $40 (Magitek Armor) (Character is shown)
CC/994B: 44 Place character $0E (Actor in stot 14) on vehicle $40 (Magitek Armor) (Character is shown)
CC/994E: 44 Place character $0F (Actor in stot 15) on vehicle $40 (Magitek Armor)

This is an instance of the Magitek Armor being assigned to Terra, Biggs and Wedge's sprites.

Open the hex editor and go to the address, and change the 44 XX YY commands to FD FD FD, which will erase, or bypass rather them getting assigned that vehicle.

Alternatively, you can use 44 XX 00 instead of FD FD FD, which is vehicle $00 (No vehicle)

You can also place the character on $60 (Raft), and $20 (Chocobo).

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-edit 1-
I found the offsets for the magitek armour for the cliff
CC/9948: 44    Place character $00 (Actor in stot 0) on vehicle $40 (Magitek Armor) (Character is shown)
CC/994B: 44    Place character $0E (Actor in stot 14) on vehicle $40 (Magitek Armor) (Character is shown)
CC/994E: 44    Place character $0F (Actor in stot 15) on vehicle $40 (Magitek Armor) (Character is shown)

But I just cannot seem to find them in the rom in windhex at ALL. Maybe I'm looking at it badly...

Searching for offset C9948 should bring you right to it. If it's not, then for the one millionth time (not to you, just in general =D) your ROM is most likely headered, so you would add +200 to the address, so it would become CC/9B48. When working in hex it's better to remove the header for the ROM so you don't have to factor in the +200 all the time, windhex has an option to do that at the top under Edit>remove SNES header - and also view the offset as SNES Hi-ROM: Option>display offset as>SNES Hi-ROM.

If this is not the issue, than I'm not sure.