I'm not really surprised. The SPU mono is a moving coil cartridge with a single coil orientated to only respond to transverse groove modulation. The Shure M55E is a mid quality fixed coil cartridge. You have fitted it with a stylus with, I assume, a pivot suspension that has a very low compliance for motion in the vertical plane.

On top of that the moving coil cartridge has a far lower output than that of the fixed coil cartridge, as well as having a different housing and mounting in the arm.

Given all that, I would expect the SPU to sound superior.