Partition Scheme advice for external HDD & Missing HDD

I have two single partitioned external WD My Book HDDs and I've just noticed they have different setups on the single partition - this is unintentional.
1.GUID Partition Table
2.Master Boot Record
3.Apple Partition Map
From the list above one is 2. the other is 3. What should they be? One is HFS+ Journaled while the other is HFS+. Reading the notes against the partition types I can't decide what they should be as it's not a boot disc for the iMac.
This problem may be related to the above?
I installed 10.4.8 yesterday (after the iLife update the day before) then having earlier formatted one of the external My Book's I ran SuperDuper to create a backup of User files. This morning I found I couldn't launch any apps from the dock or directly.
So I rebooted and all seemed well except I couldn't sleep or shut down the Backup My Book, the other My Book was fine and they're both on the same fw hub. It unmounted OK but wouldn't power down manually until I pulled the PSU. So an hour later I tried switching it on and it powers up OK but isn't mounting.
Any ideas? Dusk Utility reports OK and unmounted so it can be seen by OS X.
iMac Core Duo 1GB   Mac OS X (10.4.7)   iBook G3-800 & Airport §

Why just one?
Shopping list I can think of:
Vista: NTFS for backups and storage. Can be read by, but not written, Mac OS.
MacDrive 7: can access HFS+ from within Windows (but not x64 versions)
WinClone 1.5: to make backups of Windows from within Mac OS (requires disk image or partition to hold volume image)
SuperDuper: essential for OS X backups and bootable clone.
A drive that is used for emergency only and maybe backup partition, separate from your OS X and windows clone drive.
You can create large partitions with Disk Utility to be FAT32. Read and write in both, but not the best file system and limited to files less than 4GB.
FW800 would be fast and efficient interface. Also, eSATA if possible.

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