I used the clayton crossmember and built square 2x2 lowers and upper link with .120 dom, jjs on all body side mounts, barnes weld on flex joints on the under axle mount side (they arent great, they arent terrible either). Square tube is fine, I've been over plenty with it going on 3 years and this is my DD. A few notes to aid your decisions.
I had read that you do not need flex joints at all ends of all arms, I choose to do so, though ill likely be putting fixed ends on my axle side lowers, this will save you some money. Im not welding anything onto the axle otherwise a fixed upper would be nice to. I also have thoughts to make the passenger arm a wishbone just for extra insurance.
Square tubes have square bungs, I found most of that hardware at barnes, you could use round, but why bother when there is a better fitting option. one consideration to this would be a non jam nut style bung, one that clamps. I have not seen these in square, they might be nicer to use for adjustments idk.
Upper axle mount is an IRO 1/2" bolt iirc. It is suitable for my needs, I'm usually on high alpine areas and wheel whatever comes on said trails( with in reason, I need to drive home to hahaha). Its not a rock crawler, but it has impressed me thus far.
As far as the upper arm goes and if your welding the upper body side mount on yourself, just decide if you want the upper arm to be longer or shorter and know the driving characteristics this will give your vehicle.
An upper arm will more than likely come into contact with the floor. I made all arms out of PVC first and got a rough idea of where I wanted everything, then I bent the upper with a torch and made the bends to clearance the driveshaft and floor pan.
Test your shocks lengths comp/ext to, this might change how far your axle will be traveling!