Possible migration assistant errors and file transfer

There are essentially four different things that Migration Assistant will move (or attempt to move) for you: Applications and their associated support files, system-level network and time zone settings, Users (which includes any of the files within their accounts, most of which are what people would call "documents"--the Documents, Desktop, Movies, etc folders), and "everything else", which essentially means any stray folders at the top level of the hard drive.

Now, if you had Classic installed on your old G4, it's possible that your documents were installed somewhere other than the standard /Users/youruser/Documents folder, in which case they might not get moved as expected. The same might happen if you installed things in nonstandard locations, or if there was other leftover Classic stuff (I don't know if Migration Assistant knows to ignore Classic or not--been so long since I've migrated from a system that had it).

Otherwise, I have no idea why it would have tried to migrate Applications if you didn't tell it to--I've occasionally had Migration Assistant miss things, or mess things up, but I've never had it move something I didn't tell it to.

Depending on what you had installed previously, since the computer is pretty new it might indeed be the best idea to just wipe it and start fresh. What you COULD do, using either an extra external drive or one of your other internals, is clone the current Mac Pro system to a second drive, reinstall from the OS discs, then use Migration Assistant to move ONLY the Users over from your Mac Pro clone; this will pretty much guarantee you don't accidentally get any Applications stuff (Migration Assistant works better the closer the system you're migrating from is to the one you're migrating to), and will save you having to reimport your users or documents. Then of course reinstall any apps you need. This is probably what I'd try first.

If you haven't done any customization in your current setup, the alternate would be, prior to the above, to just try wipe, reinstall, and Migrating again, this time just checking "Users" and unchecking "Applications" and seeing if it works this time. If not, wipe and do the above.

Yes, you can do exactly this--connect them via a Firewire cable and boot the G4 into Target Disk Mode (hold down T at boot on it). Then just browse the G4 drive that mounts and copy anything you want manually.

Yes, including all bundled software (iLife, pretty much). Unlike a lot of PC manufacturers (Dell and HP, I'm looking at you), Apple ships their computers with a full set of restore discs.