I reinstalled PS2003 in order to test a recovery procedure. This was on a small farm 2 tier config. I installed PS2003 and WSS on a new server, then pointed them to existing databases.
PWA settings were intact. The only issue I had was with the Project workspace sites. Gosh its been a while, but i think I had to delete the link(not the site) in PWA, and then re add them. It was tedious. Perhaps I did something wrong during the restore process.