Best thing to do is swap to Atlas trucks. They'll lower the car and eliminate all that junk thats in the way. With 2 rail Atlas trucks, you need 1.5mm of spacers for a kadee. If you swap the MTH trucks out for atlas ones, the atlas ones come with a "button" that you insert in the truck mounting hole since the screw for atlas trucks comes up through the bottom. For whatever reason, the truck mount for the high cubes is a larger diameter than a lot of other MTH tooled cars, so the atlas button fits in it kinda sloppily. I 3D printed new buttons out of ABS that can be bonded into the floor of the car without any slop. Since it's then part of the car floor, you can run the atlas truck screws in without worrying about it wiggling around in the hole.
The quickest way to deal with the MTH trucks if you want to use them is to drill the coupler mounting hole progressively larger until its no longer there.
If you keep the MTH trucks, I think you need a 3mm spacer to lower the coupler away from the floor. With 2 rail Atlas trucks, you need 1.5mm of spacers for a kadee to match the height gauge.