Engineering your own voynich

[mja0075]

I did. It reopens the same "Polyphones" dialog.

Don't close the dialog, leave it open when clicking solve on the other window.

For the "Substitution + monoalphabetic groups" the "Solve" button displays:
Error: input dimensions cannot exceed 100 by 100

Yeah, I don't think monoalphabetic groups is what you want.
You can just enter newlines to fix the dimensions error, but it will just open a window that allows you to enter the values you want for particular substitutions as far as I can tell.