The EGR reduces NOx emissions, you weren't tested for NOx or you would have also failed that. The EGR also prevents pinging, there is no benefit from disconnecting an EGR system.
The broken vacuum valve is probably for the EGR. The disconnected EGR is not going to cause those tailpipe readings at idle, unless it's stuck open, which it isn't or it wouldn't idle.

The missing Charcoal can is not going to cause those numbers, unless he connected the two hoses together, then it's going to pull fuel tank vapors directly into the intake.

What about Pulse Air? I don't see it. What year is the truck and is it supposed to have PAIR?

Have a look at the AFM. Does the flapper close all the way with the engine off?

 

PASSED!



Much better numbers this time! I believe that after putting in the new o2 sensor and adjusting the timing, I didn't screw the distributor down hard enough.
Sunday afternoon when I was ready to give up, I checked the timing one more time and it was way way advanced. Set it back to 5 degrees and cranked that bolt down and boom, passed.

Thank you for all who helped or tried to help.

 

That's quite a difference, awesome! I'm running 3 degrees advanced and still passed. In California they (are supposed to) check the timing and you're allowed to go 3 degrees over specs. Wasn't your truck pinging it brains out with advanced timing and inoperative EGR?