What am I missing?

 Please follow my logic and tell me what I may have missed!  Stepsons 98 zx2 zetec broke the timing belt. Had it repaired for I did not want to change it in a parking lot.
 When we picked it up mechanic said "runs rough needs a tune up, do you want us to do it". Well after paying $600 for the timing belt (he took it to this place and had them do it without asking how much) I said plugs and wires no problem in a garage. Changed three plugs for the fourth (cylinder 3) didn't feel right loosening it and I elected to wait to change it till after I could do it with the engine warmed up to expand the head. One of the other plugs was cross threaded and I did not want to take the chance on stripping the fourth (I hate putting in heli coils). Old plugs did not have anti seize on them. Engine ran fine after plugs and wires.
 After 2 days (can only get over at certain times because of scheduling conflicts) he calls and says engine is running real rough as if out of gas. He is 5 miles from home and I ask if he thinks he can make it to the garage. He makes it home and we find out the number 3 spark plug is loose.
 Change the plug then no start! After scouring the bulletin boards for where to start I see that this is a common problem (no start) and that there can be thousands of things that can be not working. After reading the horror stories of people swapping out parts to no avail I started testing for everything.
 Here's where I am:

Engine turns over fine and seems to want to start.
No codes from computer (tester sees computer and communicates, every thing tests OK)
Starting fluid has no affect (seems to be spark or timing)
Plugs used are Motorcraft double platinum (as suggested the best to use on boards)
Checked timing belt and every thing lines up as it should. (timing correct)
Fuel pressure is 40 pounds and holds it. (fuel pump is OK)
Injectors getting signal (noid lights)
Coil getting signal and has 12v to center post (grounding out through computer, should be good)
Plugs firing all four (used spark tester).
Coil ohms to spec.
Seems like I have spark, fuel, and timing.
Last, as I see it, is the catalytic converter is clogged. Exhaust does come out of the end of the exhaust pipe when trying to start. Tried getting it off and got one nut off (no jokes intended). The other wouldn’t budge (using electric impact). Before I break the stud getting the cat off I want to be certain that I am not missing something. I really would hate to have to take off the exhaust manifold to fix a stud if I didn’t have to.
What am I missing?

Remove the upstream oxygen sensor to relieve the pressure from a suspect catalytic convertor. It saves breaking off exhaust flange studs unnecessarily. How did you verify the cams were in time?