I didn't beat the final boss on Masterful either, it's super impossible.
I think Fluffy might be the only one mentioned in-game (in the secret Library area), but I believe there must have been internal names I dug up, because I have this list which we definitely ignored for the most part:
GrottoRed
DeepCannons
ColdKeeper
Ghost Ring
StoneFace
Protector
LaserSystem
HydraHead
Seer
SwordFighter
Fluffy
DeepDragon
Big GrottoRed
Ninja Guy
SnowBall
White Rectangle
Ninja Guy II