In the recent past the clawback applied when one bought as an owner occupier but then rented the property out within the first 5 years of ownership. (This was reduced to 2 years in Budget 2008 but this is irrelevant here). When the clawback triggered then the owner was liable for the difference between the SD that an investor would have paid on the original purchase and what s/he actually paid (which might be nothing if it was SD exempt - e.g. new build). I don't know for sure if this SD clawback with those rules applied in 1999/2000 but I suspect that it did. You need to find out for sure and then figure out the rates applicable at the time and thus the liability outstanding. It's possible that interest and penalties may apply for discharging this liability so late.
Your original query about CGT liability may be complicated by your residency and/or domicile status. You may need professional advice from somebody with expertise in the tax codes of both jurisdictions in question.