Here are a few bits I deciphered from the battle/encounter/formation/arrangement data. I think Yousei called this "Enemy Combination Data". Boy we have a few names for things, don't we?
Encounter Table
At 70200 in the ROM.
byte 4:
bits 0-1: indicate which of the 3 monster types are initially hidden (eg Shadow dragon, what Alert summons, etc)
00: normal, all 3 appear
01: monster type 2 initially hidden
10: monster types 2 and 3 initially hidden
11: monster type 3 initially hidden
The 3 bottom bits in byte 0 are still unknown to me. Bit 0 is on some but not all of the boss battles, bit 1 is on most of the non-boss battles but a few boss ones as well, bit 2 is only on Calbrena and the final Zeromus battles.
Monster Positions:
Indexed by byte 5 in the above table, into the ROM at 71200. Each entry is 8 bytes, one for each monster in the order they appear (all monster type 1's, then 2's etc). The high nibble is X, low is Y, in 8-pixel units, with a small additional offset for X:
xxxxyyyy
- Final screen X position is (x * 8) + 16
- Final screen Y position is (y * 8).
To show my work, attached are some images I made using the data above. They're missing the +16 in X, for those with a detailed eye. The large bands of color in the background were what I used to look for patterns for the bits. You can see in the Calbrena image both of the byte 4 bits on (green and dark blue), which means "monster type 3 initially hidden", so the big Calbrena is hidden but the Cal and Brena are present. For completeness, the byte 0 colors are 0=red, 1=yellow, 2=cyan.