Wow, well researched and thought out!!!

I'd definately do what Jazz suggests and extend the rails, I wish I'd done it now (mk2 will have them like that!!) not only to cut dovetails but to put a 4th axis etc. I can vouch for putting sides on the gantry and extending them down below the rails, makes aligning the ballscrews easy (make your frame as square as possible, will make aligning easier...less shimming!!)

Looking forward to seeing this build...