I thought it would be a nice exercise to re-write the EOR function... but it's not as easy as I hoped...
To fix the program, the solution is extremely simple - use Toolkit II to modify the code, then save the modified code, and you can delete the relevant lines from the boot file!
My first impression was that some of the POKEs would be dependent on the load address - But that's apparently not the case, so what you propose would actually work, I guess.
I pretty much doubt the boot program is the original one. Why would someone do that...
No - the original boot program is not the original - I think the adaptations are to get around the copy protection scheme (although I do not recall it ever being copy protected!)