1) (This is more of a hardware question, but) Is the IDE cable supposed to be inserted so that the red cable is towards the number 1 on the motherboard and to the right-hand side of the connector on the drive?
The red or blue stripe on the cable always goes to pin 1 on both the drive and the mainboard.
2) I had to secure the hard drive to the cradle with copious amounts of electrical tape because the screw holes didn't line up. Will this impair drive performance (heat dissipation etc) in any way?
No, but you can always drill some new holes in the HD cradle so they line up
3) Are there any benefits to using Workbench 3.1? I heard that you can use it with 3.0 roms (which is what I have), and I'm thinking of getting a set of original 3.1 disks instead.
Yes, it's a lot better as there were improvements to the software
4) Recommended system and secondary partition sizes?
Personally, on my old 2gb HD (before I went to CF cards and then onto Solid State) I had a 100mb Workbench: then a 200mb partition for Work: and the rest was allocated as my WHDLoad partition. Ultimately, it all depends on the size of drive you intend to use and how much YOU feel you will need in each partition.
4) Do I install software to the system partition or the secondary partition?
^^^ Psst ... 5 not 4 :laughing:
It's better to keep Workbench and installed programs seperate
