The game does checks based on spell number when you click on the spell in the menu. Your spell is flagged as unusable because the spell ID doesn't correspond to what is expected. You should change the spells IDs in the CMP instructions in this routine:
Code:
C3/2C1E: C92D CMP #$2D (is spell Cure?)
C3/2C20: F054 BEQ $2C76 (branch if so, check for terminal ailments)
C3/2C22: C92E CMP #$2E (is spell Cure 2?)
C3/2C24: F050 BEQ $2C76 (branch if so, check for terminal ailments)
C3/2C26: C92F CMP #$2F (is spell Cure 3?)
C3/2C28: F04C BEQ $2C76 (branch if so, check for terminal ailments)
C3/2C2A: C932 CMP #$32 (is spell Antdot?)
C3/2C2C: F03F BEQ $2C6D (branch if so, check for poison)
C3/2C2E: C933 CMP #$33 (is spell Remedy?)
C3/2C30: F032 BEQ $2C64 (branch if so, check for blind, poison, and stone)
C3/2C32: C922 CMP #$22 (is spell Float?)
C3/2C34: F017 BEQ $2C4D (branch if so, check for float)
C3/2C36: C923 CMP #$23 (is spell Imp?)
C3/2C38: F04A BEQ $2C84 (branch if so)
C3/2C3A: C92C CMP #$2C (is spell Dispel?)
C3/2C3C: F018 BEQ $2C56 (branch if so, check for float and invis)
C3/2C3E: 8042 BRA $2C82 (otherwise flag spell as can't be used)
C3/2C40: 20132D JSR $2D13
C3/2C43: C930 CMP #$30 (is spell Life?)
C3/2C45: F03D BEQ $2C84 (branch if so)
C3/2C47: C931 CMP #$31 (is spell Life 2?)
C3/2C49: F039 BEQ $2C84 (branch if so)
C3/2C4B: 8035 BRA $2C82 (otherwise flag spell as can't be used)