If you add a new computer as a BDC, promote it, synchronize the domain and then upgrade the new PDC you will preserve your domain accounts.
You can then format the original PDC and install a fresh copy of Windows 2000 and then promote it to a domain controller. In Windows 2000, all domain controllers are peers, so there is no king of the domain like the PDC in Windows NT 4.0. There are no good reasons to be concerned about how the domain was upgraded. The only possible issues are below:
There are five Operations Master Roles that the first computer to create the Active Directory Domain will hold, but they can easily be moved if you need to. Again, there is little reason to move these roles unless the chosen computer is severely hardware challenged.
The DNS server will automatically be installed on the first domain controller as well, but it too can be very easily moved when the second domain controller comes online.
The first server will be your global catalog server for performing searches. Again, you can easily make more so this can be fixed if the first computer is hardware challenged.
Make sure you read as much as you can before performing the upgrade. I have successfully finished ten of them so they are generally seamless, but there are tons of things that should be done before attempting it.
If at all possible you should make sure to take a BDC offline before your upgrade, just in case your upgrade goes to shambles. You can easily promote this offline BDC back to the PDC role to recover your old domain.
Good luck.
