Well, it's a pretty involved process to remove a bankswitch. I don't think I could write a tool to do it or even give you a simple way of doing it.
You need to know 68000 assembly and have quite a bit of experience with it or you can take a bootleg/hack of it with the bankswitch removed and compare the two's differences.
I did something like that for svcchaos, comparing a decrypted P1 to a bootleg with the bankswitch removed.