"Can I use my existing IRA or does that create problems with the money already in there?"

Yes. If you do, you cannot subsequently roll the money into a new employer's 401k. If this bothers you, you can open a separate (conduit) IRA.

"What will be the tax implications of transfering the 12k from older 401k into a Roth IRA? ie. approx how much will I need to pay?"

Assuming the money already there was deductible contribution, the whole transfer would be taxed as regular income at your rate.

"What happens if I convert it to a Roth and our AGI goes over $100k in 2000? (from what I understood, the AGI to open a Roth was under $100k?)"

You'd have to "recharacterize" back to a regular IRA.
With a fee from the custodian, no doubt. Perhaps you'd like to wait until later in the year before making the switch, when you have a better handle on whether you will be eligible this year for a Roth.

Best wishes, Chris