First, the transfer question:
If you have a Panther install disc (which I think you should) transferring should actually be pretty easy. What you basically want to do is copy your old OS install (with files) to the new computer, then upgrade it to Panther immediately.
First, download the latest version of Carbon Copy Cloner. It is invaluable anyway.
Then, mount your new PB on your old computer in Firewire disk mode. Use Disk Utility to reformat the new PB's hard drive (and partition it, if you want to do that), then use Carbon Copy Cloner to clone your current OS install to the new PB's drive.
Once you've done that, shut everything down and start your new PB up from the Panther install disk. You should now be able to do an "Archive and Install" - preserving users - on the drive (I don't recommend just doing an upgrade). I'm not 100% sure about your apps, but for the most part that should get everything running again.
Important Caveats: I've done this with a G5 tower, but I used an external firewire drive to transfer my old OS to a 2nd internal drive while actually booted from the internal drive in the G5. I don't see any reason it wouldn't work using Firewire disk mode to put it directly on the drive, but I haven't tried it. Since the PB is new, though, the worst you should be able to do is entirely erase the PBs drive, and you can just reinstall anyway.
The other caveat is that your apps might install system stuff that doesn't get transferred in an Archive Install of 10.3. If that is the case, doing an Upgrade install might be the trick, but there's at least a chance it'll cause problems down the line, so reinstalling any malfucntioning apps after the archive install is probably a better idea.
As for firewire drives, there still seems to be some lingering issues even if you upgrade to 10.3.1 and upgrade any FW800 drives' firmware, so I'd be cautious. Them being formatted under Jaguar shouldn't make any difference, though--the issue is with Firewire in general, not with they way they were formatted. At the very least, I woudn't restart with any external drives attached, just in case.
