It certainly sounds like an "interesting" one
Given that the programmer has gone to the trouble of encrypting the code and data, I'd guess that there will be multiple checksum routines and they will be well hidden in other (probably vital) routines.
Did you try leaving the copylocks themselves untouched but patching the actual bsr/jsr/whatever to the copylock routines?
You could look for slightly odd instructions that might be used to calculate a checksum - eors or shifts for example - but there will be many innocent instances of these too. I'd also check the interrupt and disk loading routines as possible hidey-holes.
At what point in the run does the game crash? You basically need to trace all the calls from the copylock call to around that point and see WTF the code is doing. It will take time, patience, dedication and lots of coffee.
How was it originally cracked? I'd say: time, patience, dedication and lots of coffee
You'll probably kick yourself when you do find the checksum routines, but it should make a good tutorial!
I notice there is a WHD patch for it made by Mr. Larmer and updated by Dark Angel. Wepl will have the source code for this...