Dave,
Yes, ability stats are carried over from BG1 to BG2.
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As for the abilities gained at the end of BG2:
Your "Final Save" (which the game generates) is, as Father Bronze hypothesized before you get the end bonuses. So...if you want to carry over those special abilities, I suggest that you save a game just before you use the last Tear. I suggest this because in order to have the bonuses reamin in ToB, you will have to replay the final fight with Irenicus and go right into ToB from there...after the end movie. That info. is direct from the Black Isle designers on their boards...
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Now where did I leave that doughnut?!