This is my rotary situation.
I have a t-track bed with well cut mdf inserts that the whole contraption fits into that I remove when using. I’m going ot assume you have a similar design. One thing I would look into for feasibility is remove most of a slot. It puts it down in a repeatable location meaning i can add location specific information placed in the post processor and using work offsets, i don’t have to rezero it again.
I have a piece of 1/8" or so aluminum plate that I attached to the extrusion, I then attached the headstock to that piece of aluminum. For alignment, a piece of machined metal (or even wooden dowel could work if you get a truly straight one), clamp it in the jaws and align the headstock with the tailstock, and tighten the headstock down. I use clamps to hold down the whole assembly when using, and also tuck the wires inside that gap to keep them from being tripped on.
If you alloted slot is oversized for the slot allowance along the Y Axis you could use something like a piece of 1/4" ply just to get the spacing good. If your spacing is undersized well… that sucks and i dont have an idea.
More information on my setup can be found in the rotaries have arrived thread… starting here: