Sorry, long time since I put them in, do not use the spacer, stick shock through, install the larger of the two collared spacers from the top, install nut. that should locate the shock stem and give you plenty of thread. The shock stem seats directing into the shock mount.
10 speeds need to be put together is a surgically clean environment. The OEM ones are done in a sealed room. Bad things usually happen when they get taken apart and set on random shop rags. The replacement transmission should have had its own warranty?
Have you ever noticed your brake lights staying on intermittently? Not sure it effects your model year but it causes similar problems and is a very quiet recall. I currently have a zip-tie in there. The little bumper disintegrates over time making it get worse. Then when it fails completely...
The rotors are in stock at most dealers, not on national back order.
I show 23 front rotors available same/next day locally to me, 12 rear rotors. That's just from one of my warehouses.
The G-LOC suggestions are inaccurate. R14 pad is for Formula Ford cars, not heavy high HP cars. Not sure where the recommendation for not using R8's or R10's on the front came from, those a massively popular. Not everyone is trying to win an HPDE trophy.
Pictures help, but if you put the backing plates on a flat surface and they are flat, it's just expansion and contraction. Curbing and clearance issues can bend a backing plate via the brake pedal. Depending on the pads, the majority are molded since late 2023. They use a patented backing plate...
Just buy the knuckles from your local Ford Dealer and our Hubs. We have a love hate relationship with Ford parts, we usually lose money because they change prices constantly.