Hi "snyth". You should have posted this a new thread -- you're much more likely to get more responses.
FW400 is at best borderline (throughput) for an Aperture Library. It will work, but is far enough from ideal that it is not otherwise recommended.
If you have room on your system drive, I recommend putting your Library there. That is, in fact, how you probably should have started 😉.
Then, if you begin to run out of room, convert some or all of your Images' Masters from Managed to Referenced.
As you point out, any Referenced Masters will have to be backed up separately from the Library. (The Vault backs up only the Library.) Figuring out the best way to do that varies by installation and available options, but is not hard to do.
It is rarely helpful to split a Library. You want to be able to do global searches. (Imagine if a real Library took the books on each floor and moved them into separate buildings, each with their own card catalog.)
It is -- as far as I know -- impossible to have too many Images. I've used Libraries with almost half a million, on machines w. just 4 GB of RAM. There are surprisingly few bottlenecks -- a testament to Aperture's architecture (and designers).
Lastly, you shouldn't have the number of problems you are having. Move (and consolidate, if necessary) your Library, get it to work, give it some time to settle down, and see what happens. I have never experienced a downside to running "Repair Permissions" and "Repair Database" -- I recommend that you do that once you have moved you Library and created a new (and redundant -- save the back-up of your current set-up) back-up.
Good luck. Post back with questions, and with your results.
Message was edited by: Kirby Krieger -- a few changes for clarity; link added.