I would verify timing before I pulled the heads but with low compression on a couple of cylinders it might make sense to just get the heads done and be done with it. Just the ramblings of an old man….
I picked up a set of paper ones for an '03 Mustang including wiring manual on Ebay a while back, they were barely used, I don't think the wiring manual was ever opened.
Glad you found the issue! Nice to see someone stick with a problem till they find the root cause. Lots would have given up and taken it to a shop. Congrats.
Odds are those are Stover nuts. They are a type of lock nut that pinches the threads on the stud so they don’t come loose. If you look at one side you should see that it isn’t round, more of an oval shape. The other side it will look like a normal nut and will thread on easily till it reaches...