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.
I had a similar issue. What 6L6 says is always the solution. Better yet: Never tighten any of the screws when doing this kind of assembly until everything is properly aligned.
