I notice on your design the X rails are the same length of the box seciton. I would leave about 5-10mm clearance at both ends to ensure they lie flat in case the box section is distorted at the ends.

Going by your order;

1) Bear in mind the holes in the SBR rails look like they've been drilled by an ape swinging on a pillar drill - you can sometimes even see the pencil lines which mark where the holes go, so don't expect them to be accurate. Make the frame and gantry then mount the rails to the frame by drilling and tapping one hole at a time until you have them aligned and running smoothly, then drill and tap the rest.
3) I found recently that a local shop is cheaper than getting the pulleys and belts online, plus no long delivery time and additional delivery time to send back the items they got wrong!
6) I reckon try LinuxCNC then mach3 then Planet CNC because clearly if you get on well with LinuxCNC then you've saved a lot of money compared to the other options. If not by all meant buy mach 3. Either way don't expect to learn much if anything about Linux though, since one it's installed it's just like using a program on windows.

Foam is an interesting idea, by all means try it but I don't think it would help that much with resonance. As far as I know the issue is not the 'air resonating through the centre', it's the walls of the steel box section that vibrate. To prevent resonance on the not moving parts you should add mass, or some material with good damping properties which tends to be materials made up of particles which rub against each other to dissipate the energy as heat. Sand covers both criteria, but it sounds like that's not an option.