Illustrated guide to the 4U deluxe Chassis

The stamped brackets that are attached to the heatsinks are the spine into which everything else attaches. If those are off, the rest will be. A little bit of adjustment there will make big changes to the whole.
 
I suspect that It’s All In My Head’s step 3) is pretty close to what’s needed - remove top and back, loosen the bracket screws, square up everything, tighten brackets, reinstall back and top.
 
Did you buy individual panels and not a whole chassis?

Regardless, you’ll need M4 machine screws and nuts, M3 machine screws and nuts, and depending on the style of heatsink brackets, some M3 self-tapping screws.