Hi Pari,
The bearings that probably are still on the gantry after you removed all those bits in your photos. Still trying to figure your stuff out...
Yeah, your's is way different than mine....except that the limitations of mine are largely also built into yours....but mine sort of has to be the way it is due to my bearings (their is one rod on the top and bottom of my gantry beam, so it needs to have a rigid connection between the two...and the original rigid connection was the Z linear rods).
If you can lose the red part and keep the rest of the aluminum, I would just make a spacer (if needed for clearance of any bits) and then buy a pre-assembled Z axis, mount the motor you have, then mount the spindle....you might be able to reuse the existing spindle mount plates, but not sure.