Ok, I ground down the lip quite a bit to get a bit more clearance and that helped it fit the base plate a bit better. I have managed to get the head & body looking a bit more even (I think) with about the same gap, which I am ok with. Tilting the mechanism backwards only made the gap at the front worse as the body is already tilting forward.
I still have the issue of the stalk preventing the dome being installed correctly, so I am going to have to extend the hole that the motor sits in to be able to shift the whole thing backwards.
I decided to connect everything up and test it, so in test mode all was good but when I exited back to attract mode, the motor runs continuously, started a game and the motor still continues to run. Any suggestions on how I solve this?