After Installing Windows 2000 Pro, I removed the default security permissions on each of my partitions (Everyone - Full Access). I then applied custom permissions to the Administrators local group, SYSTEM, and Creator Owner. Since everything in WIN2K/NT is done by SID's, will I effectively lock myself out of my own partitions if I reformat the primary partition and install XP?

As far as I remember no you wont.
Once WinXP is installed you'll simply be able to "Take Ownership" of the folders and partitions where you've set custom security.
However
If you in turn encrypt any of these folders and/or partitions you will not be able to access them unless you first backup your keys to floppy and then re-import them into WinXP.

Builtin groups should retain the permissions and you can also take ownership of the custom folders and grant new permissions.