[wrndln]

Do you have the long studs that are threaded into the brackets inside the holes toward the back? There are brackets that slide onto the studs to support the top irons. That should allow the top irons to rest on the studs/brackets keeping the top from resting on the spare tire. See picture. If your top irons are originals and the studs/brackets are the correct one, I would think the window wouldn't rest on the tire. After looking at your second picture again, it appears you do have the top rest parts installed, so I am not sure what the problem might be.
Rusty Nelson