Are you saying that the ball screw nut is too wide to fit in there? Or are you concerned about the timing belt pulley? If it's the latter, it doesn't need to be in between the bed and base - it can mount outboard from there. If it's the former, you can either shop for a ball screw with a slimmer nut, carve down the nut flange a little, make a groove in the base plate for the nut to run in, or use spacers to elevate the trucks.