Do your REF headers have 1-7/8" primaries or 2" primaries? We mocked up the REF headers on the Mustang this weekend, our Mustang also has shock tower reinforcement plates, but they fit actually super well. Ours are the 1-7/8" primaries.
We wrote ourselves up a whole procedure of the order we put everything in. One thing we had to do is drill a hole in the shock tower for the #5 top flange bolt, it was impossible to get that bolt in without doing something like that. At #3 the shock tower also required some grinding on the reinforcement plate, and we slotted the top flange to get the bolt in better.
Tube's went in one tune at a time. Drivers side, #7,#6,#5, then #8. Passenger was #3, #2, #1, then #4.
Picture's don't show up too well because it's black headers on black engine compartment.