Ah OK. It's not too clear from the photos exactly where the holes are.
I think you are right to leave off the square spacers and make your own. A bit of rail or an "L" shaped bit of brass sheet of the right width would do the trick. You could make a couple but leave them loose until you know where the motor/gearbox will sit.
I did something similar to my Deeley Dock Tank build, but I repurposed a motor mounting spacer as a frame stretcher to take the compensation pivot: