If you are going to install the motherboard in a tower anyway, then go for a 3.5" hdd instead of the 2.5" hdd that is recommended for desktop model. Get yourself a 2.5" --> 3.5" hdd cable adaptor. You will need it to get the 3.5" hdd going, and while you are at it you can install a CD drive as well.
As for floppy, get yourself one with a faceplate. Don't expect all PC floppy drives to work straight out of the box though, but some can easily be modified to at least load AmigaDOS disks.
And to your last question; no, you do not need to install Kickstart3.1 roms before you install any drives. You only need to upgrade to Kickstart 3.1 if you are up for it, or want to install OS3.5 or OS3.9.