I am a big fan of using red oak instead of MDF on the smaller machines. I spent around $90 on red oak for my first effort, the Solsylva 25x37 and it was well worth it. If you need a 2x4 just laminate two 1x4 pieces. It is much stiffer than MDF, poplar, or pine lumber and looks much better than the others with clear finish. Bolts don't crush the oak when tightened securely. I consider it to be a lower cost material versus aluminum that is almost as good for building these machines. For no more oak than you used on your 10x9 the cost is not much of an issue at all for what you ended up with. Looks good.
If you want 35" x 35" cutting area, draw a square of that size as a "keep-out area" and then draw everything else around it and include any additional distance you need for limit switch operation. The center of the cutter should be able to cut around the 35" x 35" square on all sides. You will find that the amount that the cutter is forward of anything on the gantry that causes interference in the rearward travel, and the width of the Z assembly will interfere with the sideways travel, needs to be allowed for.
One thing I found with the DW611 is that the big yellow head on the router will need to be allowed for so that it can be raised to full Z height without hitting a motor mount plate at the top of the Z assembly. My router mounting plates could be 1/2" shorter than they are now if I had purchased the DW611 sooner than I did. The Z assembly had already been built by then.
It depends on how far off center the holes would be. Can you stagger the holes, alternating between two 8020 slots or just make two rows of equally spaced holes? CNCRP carriages need at least 1/2" of the rail edges overhanging the 8020 beam on each side.