Anyhow, these are my thoughts on the matter. I know very little about how item-crafting is done in D&D and since so much else is altered in BG, I don't really aim to emulate it but if anyone knows stuff about it that might fit into this, feel free to tell.
First of all, I think it would be most fitting as a bard kit. It might seem kinda strange seeing as it doesn't have a whole lot to do with music but I think basing it on bards offer some other interesting pros. A bard is a pretty lousy fighter with high lore (is it possible to change the amount of lore a kit gains per level? If so, the Crafter should be the motherfrakkin king of identifying) and no thief-skills beside pick-pocketing which seems good. The bard song button would most likely be disabled unless someone comes up with a really cool version of singing that fits a crafter. Spellcasting would either be disabled or heavily specialized (see the paragraph below).
Now... a question for people more skilled at coding then me. Is it possible for a spellcaster to only be able to memorize a very limited number of spells? It seems reasonless but I've never looked into custom kits much so I'm not sure. If so, that might be the best way to go about with the actual casting. A crafter would then be able to find written recipes (my not-quite-fancy name for crafter scrolls), learn them and then craft stuff through spellcasting.
Related to the above is the question on whether or not crafters are magic-users. It's an easy way to explain how the create really fancy stuff in a fantasy-setting but on the other hand it would be nice to separate them from the gazillion kinds of magicians that already exists. Thoughts?
One of the few things I do know about D&D crafting is that you need both physical components and (I think) sacrificing a bit of XP to build stuff. This is something I'd like to keep for a BG crafter. Since buying stuff for everything you're going to craft would be goddamn annoying, it'll probably just drain a bit of gold. The XP sacrifices wouldn't be very heavy most of the time (maybe a couple of hundred XP for a minor item and a few thousand for a somewhat powerful one).
As for what the crafter (most likely a temporary name by the way...) actually would be able to, well, craft... I'm not entirely sure. First of all I'd like to throw in a bit of alchemy. I've always thought that it's a little annoying that the Create Potion HLA or whatever it's called doesn't become available until a lot of the potions you can make doesn't matter much to the gameplay. So potions for healing and other boosts would probably be among the first things a crafter could do. After that it would be reasonable to have some fighting-related stuff since a nerfed bard isn't much good in a fight. I don't have any concrete ideas yet but stuff similar to Jan's Bruiser Mates and the pantaloon-bazooka-what's-its-name (i.e. projectile weapons with neat effects) usable only by the crafter could probably be nice.
Another thing that could increase a crafter's usefulness in combat would be the ability to create some sort of pseudo-familiars that can fight his fights for him so to speak. I'm not sure what those would be like (although golems come to mind). If that living-chain-creature mentioned elsewhere is released it would be tempting to have them as an alternative.

Then, of course, there are "normal" magic items like magic weapons, armors, rings, etc. that everyone can use (or sell). While I'm having a hard time coming up with a good in-game reason, these should probably be one-off abilities (or very costly ones) or a party with a crafter in it would raise the Shadow Thieves/Bohdi's Guild money in about three minutes.

There could also be items that need actual components to be made, similar to those put together by Cromwell and Caspenar. Either a crafter of sufficient level could make the same items as them (free of charge! Yay!) or additional magic items in need of assembling could be put into the game.
The kit should probably have it's own HLA list full of epic items they can make.
Ehm... I'm sure I've thought of more stuff as well but I can't think of it right now. I'll probably add to this idea-list later. Until then... gimmie, gimmie, gimmie feedback.