As always the most important part in any project is coming up with a plan. Doesn't have to be perfect and it doesn't have to even be finished. Just have a rough design and plan of action.
I planned out the rack in Autodesk Fusion, and then uploaded and scaled an image of the jeep so that we could test the fitting, In our plan we initially wanted to be able to hide the spare tire completely in the luggage rack, but found that the 9" height to do that even though it looked good on the computer was just way too tall so we decided to change the height to 6" even though the plans don't reflect that. Though we strayed from the plans it was still much easier to have them as a starting point.
Step 1: Cutting and Assembly
I've always found it easiest to cut all the pieces that you need ahead of time rather than cutting and assembling one piece at a time. We used a harbor freight band saw to make sure to get all the angles cut accurately and aside from the saw giving us a few problems due to stripped out cast iron threads it actually did a very good job.
When you go to weld everything together make sure to lay out the bottom section of the frame, and use magnetic squares to hold everything true when you tack the corners. Then you can measure from corner to corner to double check that everything is true and straight. When you're happy with the bottom frame you can weld it completely, grind the visible welds smooth (top bottom and outside) and set the components for the upper frame on top of it and tack weld them together using the bottom frame as a jig.
Next you can go ahead and weld on the middle supports, I would suggest cutting a couple of pieces of wood or metal that are the exact size that you want the middle to be, for us we wanted 6" total from outside to outside, our material was .75" thick, so the pieces we cut where 4.5" long. I stuck them in between the two frames and clamped them in place. then welded the uprights in place.
To attatch it to the vehicle we used a piece of .25"x1/2" flat bar about 5' long on each side and bolted that directly to the roof of the jeep using the existing holes used for the original utility rails. The jeeps roof has a slight curve to it so we needed to place the rack where we wanted it and measure from the bottom of the rack to the top of the mounting bar for each point that we wanted to put an upright.
Step 2: Paint and Decking
Next up you need to pull the rack back off the roof, paint the frame, and build whatever kind of decking you prefer. We talked originally about using expanded metal, but thought a nice sealed wood would look good and it turned out looking very nice I think.