That's pretty cool!
Is this to verify that there is no tampering with the file, or is it just one of those cool things you wanted to add?
Either way, godspeed, my friend (unless it's already done, which in that case.. . um. .. Good job)
through some experimenting(and a few secs/mins, depending on how big the prg file is), the checksum now drops every character of code XORed into only 32 characters, nice