It's been a while, but most of that *should* be pretty easy. It's just a matter of knowing which files do what. Generally they're in the override folder, but you may have to extract them using bifextract (?) - as I said, it's been a while. All the relevant files are just text tables.
All of the weapon profs/usage limits can be done REALLY easily - as can the backstab multipliers. The armour usage is OK anyway (that's the default for theives). Use any item is going to screw with any limits you place on item usage - from memory I think some items have limits on themselves (usable by) whilst some classes have limits (cannot use) and it's not particularly easy to do.
The theiving skills bit is more of a problem - you're either a thief or not, os it's all or nothing (these are harcoded by character class, not kit). Set traps could be assigned as a special skill for anyone (I once gave my assassin the Kensai's kai!), but to be honest I don't think the other skills are against the concept - how does he break into a house? Does he avoid the traps left there? What about non-lethal missions? Assassins don't *just* kill.
Sorry about the vagueness - most of what you want can be accomplished in a matter of minutes (I've done very similar in the distant past), but some is impossible.
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