Never confuse your disks with your discs.. That would be bad. :-) I couldn't work out whether your tower had a CD cus obviously you would need CD access to install plus 3.5 and 3.9 need the CD.
I still use 3.0 on my 1200 and thats got like 2 external SCSI drives, CD Drive, ZIP drive and is on broadband and networked to my PC computers. Been with me since 1993. I have machines with the 3.1 ROM and the 3.1 Workbench but there really isnt that much difference. And sadly an unexpanded 1200 with 3.9 or even 3.5 is really slooooooooooooow.
Sorry I must have missed your other posts. Don't know really what you are driving. The install simply allows you to install all your 3.1 disks onto the HD so you would need them all. I assume you have 3.0 already on the machine so you will not need them, though I would back up your Workbench on another Vol on the machine if you can.