I have some software at home to connect an Amiga to a PC via the serial port for printer/CD ROM/RTG/Clipboard/HD access. When I get home I'll test it. My only worry is memory as I'm not sure the 1.5MB will be enough.
I stripped unnecessary files from Workbench and I had Ncomm running off of one or two drives because I never owned a hard drive on my first Amiga 500.
My Commodore 64 had the following protocols: X-Modem, X-Modem CRC and Punter. I know my Commodore 128 had the Y-modem protocol in the terminal program and they didn't have a lot of memory so it is a shame that you need more memory to do the same thing.
I bought my first thumbdrive from Lexar. It was a 128MB thumbdrive and I had to download a 5 megabyte driver. Drivers since then aren't that large and I know they are more complicated machines now but if you can't use existing Rom calls or Kernal calls in your Amiga then you will have a large program but a program has to be simple with just what you need and no more features.
I think that even a dumb terminal program with a null modem cable can make your Minimig function with file transfers using the IBM PC.
The Minimig board needs to be expanded in my opinion. Even if you make one that isn't fully compatible with the old stuff, you will have some of the same characteristics but possibly more powerful in a new machine.