I'm sorry to say this, but I doubt this will be the last problem you get with this install.
Both professionally and privately I've never known an upgrade of 98 to 2000 go without a problem (usually pretty terminal ones). If you went from NT4 to 2000 I'd be far more confident.
It's useless advice to get in hindsight, so sorry
, but it may be worth keeping in mind that a clean installation will always be better.