Bad Drive, Enclosure or Firewire Port?

I have a WD "Book" drive connected via a FW800<->FW400 cable to the FW800 port on my mini. After having the 10.6.3 upgrade go south on me, I'm having problems with the drive. I was able to get the mini back-up by reinstalling 10.6 and then updating through Software Update, but I'm still having troubles with the drive.
All tests give the drive a clean bill of health, but if it's connected to the machine, I cannot boot the Mini -- It starts to boot, but never doesn't get to the login screen unless I unplug the drive. I can mount the drive after login; however, eventually some application access the drive will "space out" regarding the disk access. It seems like any part of the program that's not related to the disk access (UI, other windows, etc.) will continue to work, but anything actively involved in, or waiting on the completion of the disk access will stop making progress and never complete. For example, copying files in the Finder will stall eventually (it might be after less than a dozen files, it might be after a thousand. I was able to get all the files off the drive, so it's not corrupted files/disk.
Before the upgrade troubles, I was planning on pulling the drive out and putting it in another enclosure (I'm not too happy with the WD Book enclosure), but now I'm hesitant. If the stalling problem is due to the enclosure, I'm OK; however, if it's the drive, then I'll have to buy a new drive.
My big fear is that something horked the firewire port and/or software, so attaching anything to that port will cause problems. Short of borrowing something to run on the FW800 port, is there any way to test it?
Ray

From what I've heard, the MyBook is not a drive that can be used outside the case, but is hard-wired to the enclosure.
That said, there are disk maintenance tools that can fix and repair directory structure, notify of bad sectors.
Or maybe it is cable, or FW ports, and needs to be reset.
When SL came out it seemed like there were an exceptional large number of reports of problems than would be expected, often from 'known' good brands using Oxford chipset (not sure if they were the latest, or if the latest were the very ones having trouble), but there have always been the fear that another 10.3.0 FW bug would occur.

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