Does your MPU work? Does the pin boot and at least go into attract mode?
I am not very familiar with system 11 systems, but I think the earlier boards will work in all of the later system 11 games. The earliest system 11 boards had the most parts and later boards removed more and more sections. If you try to use and earlier board in a later pin some connectors will just not be used.
I know I was very happy that my Pinbot came with a system 11 MPU board in it (I know some need it, but mine did not, it was a later replacement), I was able to steal that board and put it into a dead High Speed that needed it. I don't think a system 11 replacement board is available yet, I know when I stole the board from the Pinbot one was not, but system 11a boards were available. So the Pinbot got a new Rottendog board and I had two working pins.
This seems to be not that uncommon to find original system 11 board in later system 11 pins that don't "need" the earlier board. I won't name any pins in particular, but if you look at the other games that used original system 11 boards only HS seems to be a popular title. I think many of the early system 11 games were cannibalized for boards for later, better earning titles. Just a random thought, perhaps an operator can chime in.
But if it were my Earthshaker, I would buy a Rottendog board and sell your original system 11 board so someone can get an early pin that needs one and does not have a replacement available. I got a good price for my "dead" system 11 board. I would think you could get a very good price if yours is working, it would probably cover most of the cost of a new MPU.
Hopefully a new MPU will eliminate some of your problems and get your pin working.