Just a couple of quick answers as I have my A3000 running:
When you boot into Workbench, hold your right mouse button down and then under the "Workbench" tab select "About". A small window will open and it should state your Kickstart version. I have Kickstart 3.1 ROMS so it reports Kickstart version 40.68.
To get rid of the PC0: floppy simply go into your "SYS:Devs/DOSdrivers" draw and drag the "PC0" driver back into the "Storage" draw (I wouldn't delete it as you might want it later).
Personally, I'd leave it in there as you might find it useful for transferring files from your PC to the Amiga. You can download a file on the PC, copy it to a 720KB formatted PC disk (not a 1.44MB!), but it in the Amiga and it will appear under PC0:. So, if you have an Amiga DOS formatted disk it will appear under DF0: and will look like junk under PC0:, if it is a 720KB MS DOS formatted disk then it will appear under PC0: and look like junk under DF0: and if you have a custom bootblock Amiga game disk that has to be booted at startup then it will probably look like junk under DF0: and PC0:.
HDToolbox will take care of those MAC and PC partitions on your hard drive (Remember that PC0: is not on your hard drive - it's your floppy drive), but make sure that you have your Workbench disks to reinstall your OS later. Surely you can just click on the MAC partition, select format and then format it as an Amiga FFS drive without repartitioning?
Some old floppy games don't like Amigas with newer Kickstarts and neet a program to load an older Kickstart into RAM for them to work (Relokick1.3, etc). However, I get most games to run to the A3000 by doing the following:
Reset Amiga
Hold down both mouse buttons as it tries to boot
On the Early Startup Control, go to Boot Options and disable the Hard Drive and CPU Caches. Click "USE".
Under Display Options change it to "PAL" and "Original". Click "USE".
Insert the floppy disk into DF0:
Click "Boot".
Keep your fingers crossed.
