Microcarve has really hit on something with the threaded rod putting MDF in compression. I just fitted the gantry cross beam to glue the two pieces together, and it is impressive how rigid the frame is already.
Since I didn't finish the CAD model, and wasn't sure how much overhang to leave between the spindle center line, and the gantry beam, I haven't cut off the excess MDF on the side panels yet.
Rather than CAD modelling (sometimes I really like it, sometimes I like fit and see fabrication), I just laid out my rails and ballscrews and guessimated the overhang.