Taillow I still have my old copy of TSCA too; I was at work though so I couldn't check. <_<
Is there anyway to program passive effects onto characters or equipment? For example, giving certain weapons and characters a damage bonus when attacking certain enemies. Or even weirder, modifiers to damage inflicted or taken if the en enemy's level is higher than the characters.
For weapons you can set a particular element or elements for them and set individual types of enemies to be weak against them. For elements there are five (six in XP and VX) different modifiers: A, B, C, D, E (and F for XP and VX), where A is very weak, B is weak, C is neutral, D is strong, and E is immunity (though you can change the modifiers for each letter; the defaults for weapon elements like slashing are A=150%, B=125%, C=100%, D=75%, and E=50%, whereas for magical elements like fire the modifiers are A=200%, B=150%, C=100%, D=50%, and E=0%. In 2003, XP and VX it's possible to set a negative percentage for the modifier to indicate absorption). You can also change the modifiers as you see fit.
Sample screenshot from one of my games (EDIT: no longer online; see attachment):
Regarding extra damage in regards to level--you can't set a "level" for enemies from within the interface; the only options you can change regarding numerical stats are HP, MP, Attack, Defence, Mind (Magic Attack and Defence), Agility, critical hit chance, experience, gold dropped, and item drop chance.
Another screenshot (EDIT: also not available; see attachment):