Let me see if I'm tracking....
On the current design you cut the arm mount down are are just thinking of mounting it direct to the tower? If so what if you got a thick piece of aluminum or steel plate and directly mounted the arm to it. That would solve the height issue by creating a spacer and should be stout enough to support the forces be placed on the arm. Basically retain the front bushing set up and then would need to do something on the back. If you could use a bushing instead of just a bolt it should improve shift feel (I'm guessing here).
OR.....
Just fab your own out of a plate of steel. Determine the diameter of the shifter and make a new socket for it.
Something like this silly thing I drew
