The hitachi drive issue was resolved with firmware 1.03, so you shouldn't see any problems.
The only thing I might do different is: If you are not setting up a RAID, then just pop one drive in the enpty bay. Format it and it will become Volume_2. You will need to choose if you want EXT2 or EXT3 format and you should read about that in these forums if you don't know the difference. If you have data to transfer, do that next. Once done then remove the original WD drive and pop in the last new drive. Format it and is should become Volume_1. Now you have your new drives installed without reseting to factory defaults.
You could also setup a RAID 1 (not RAID 0) by the same process above. It's slow during the mirror process but it can be done. That's what I did actually.
If you are looking for RAID 0, I think you need to start from scratch but since I've never done that, maybe someone else have a different view on it.
Hope this helps the transition.
-Joe