Just to be specific here, you're actually having slow logins, not slow startups (well, the startup is a bit slower, but I concurr that it's due to more RAM while it checks it, but that doesn't explain the login.)
I didn't see anywhere here that you'd tried creating a clean user and timing the login to that. If you haven't, try it and compare; if the new user with absolutely nothing in it still takes a long time to log in its either OS or drive related. If it's fast, then it's definitely something about your settings on that user.
Also, is it just as slow when you log out and back in? That'll also narrow it down a bit.
Incidentally, the amount of stuff on the drive should be completely irrelevant unless (and really, even if) you're using Spotlight as part of the login process, which you're not. The only thing that matters significantly is free space, and assuming that the HD1 you mentioned is your boot drive, 9GB should be sufficient (in any case, as much as the PB has).
The faster login from the FW drive could be due to a severely fragmented boot drive, bu I'd be more inclined to think it's because of something cached that didn't get cloned.