You don't have to keep using AmiKIT, just use it to create a new HD file, set up a vanilla OS3.9, then use that instead. One major advantage of AmiKIT is that it is a painless way to get a working Amiga environment, even if you don't want to use it in the long run.
Edit: Do you have a real Amiga? If you do, you could connect it's HD to the PC and boot from that. Also, you obviously have a Kickstart image, couldn't you get 3.1 from the same source?
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Ferrari 312 specifications
