If I play a thief in classic BG1 (no kits available) what happens when I import into BG2? Can I select a kit then, and if so, does it backtrack all of my levels as if I had always been leveling up with that kit? Also since not all skills are available (like set traps) do I get to reassign my skill points or do those stay as I would set them playing as a theif?

You get to choose a kit, and if you do choose one, then you get all the bonuses as if you'd been that kit since level 1.

You also get to reassign any skill points, spells, and weapon proficiencies, as many of those changed or were removed in BG2. Large Swords proficiency, for instance, is broken into Two-Handed Sword, Long Sword, Bastard Sword, and Scimitar/Wakizashi/Ninjato, and Stealth is split into Hide in Shadows and Move Silently.

The same applies to any other class except specialist mages. They're already "kitted." You can still move skill points around, however.

ANY character you export from 1 to 2, at Shadow of Amn's character creation screen, you get the chance to select an appropriate kit for. Fighters, Paladins, Clerics etc are in for it. Even already dualclassed humen will be able to choose a kit for their inactive class, but it wouldn't be bright at all to dual before 9 or 13 level of XP. (About dual-classing to mage, in 1, if you dual class to mage, you can dual class to a specific mage school if you wish for it; unfortunately enough though, in 2, you can only dual to mage exclusively.) So the need for cheating and shadowkeeper-ing is totally eliminated this way.

If you want to enjoy your gaming experience to the fullest, don't bother with mods, trainers, cheats and cheesy addons that are not official. TuTu and Trilogy mods, besides having bugs of their own (despite addressing and correcting many previous ones), needlessly change your gameplaying experience. Why not enjoy 1 vanilla and choose your kit/dual in 2? Rules and regulations are musts for roleplaying. And that's what this game is all about...