Actually, you do not have to change your heater core.
There are a lot of FAQ's on the internet about this swap that say you have to swap the heater cores, but you really don't have to, because they are exactly the same 96-98 and 99-00.
What you do need to do is:
You need another heater resistor and the 'high relay', temp control motor (CRV 97-01 is the same as civic EK), climate control wiring harness, other plastic center vent duct, and off course the climate control center panel itself.
The center panels are pretty easy to find on Ebay. I got the temp control motor 2nd hand from a junkyard, and the rest I bought new from the Honda dealer (I have acces to EPC, so I sought out all the parts i needed)
It's not an easy job. A couple months ago, i've done it on my civic (it is a LHD, but i guess it will be similar for a RHD).
It needs some rewiring (for hazard warning switch and the rear window defroster button).
And you will have to remove your dashboard, in order to install the other center air duct. (because in the 99-00 center panel, the vents are located a little bit more to the side).
It's taken me about 2,5 days to do it (I had to sort out the rewiring) and I did it very carefull and slowly.
But still it is quite a big job, because of the dashboard that has to go out...
Far more difficult than changing stereo's, but I would be happy to help you out if I can