I would seriously consider getting a new accountant. That overpayment may have cost him close to $200K.
see my comment 20 - it sounds like he withheld the 20% max long term rate on the option exercise/sale, which if he didn't know for sure how much he would give to charity was reasonably prudent.
that said, I don't know what his AGI was in 2004 and thus don't know what the safe-harbor withholding would have been.