Thanks for the feedback. Yeah, that's the part that I'm struggling with. The way the pinion has to line up with the rack means I have a particular thickness I can use to join the upper and lower carriages if the R&P drive is going to mount to the outside as shown in the pictures. In this case it's 5/8", so I can either do hardwood, plywood or MDF. I want to thicken the gantry sides above the top carriage as much as possible (like I've shown, but maybe all the way to the inside edge of the top carriage) and bolt the thickened gantry sides to the top of the carriage in addition to the side. I could do 5/8" aluminum for the sides if I have to. I wonder though if that would be stiffer than having the sides be 2-1/2" thick from the top of the carriage to the bottom of the main gantry beam. I still haven't thought much about the connection between the gantry sides and beam.What ever your gantry sides are made of, they look like a weak point. Are you using hardwood? Whatever it is, it need to be thicker than the 3/4" it appears to be. Especially where the top carriage is bolted to it.
I was originally thinking of doing something like this older screenshot I made, but I read a comment that said it's better to have the gantry overhang the sides so that the carriage bearings aren't pulled out of line with the 1/4" rails...