Well I confirmed that the EGR and the charcoal canister purge are operating when the car is driven.

I climbed under the car and noticed flashing around the spark plugs on the passenger side. Particularly around #8 and #2 or #4. I suspect this may be my problem of rough idle. It would also exlainthe ticking sound from the back of the block. I am not sure why it clears up when the car is driven a short distance but I think the PCM is compensating for the missing cylinder when the O2 sensor comes into play in closed loop mode.

I am going to replace the plugs and wires and see what happens. I did not use dielectric grease the last time I replaced them but I will this time

I plan to use the OEM wire routing. Any recommendations on wires that will fit in the stock wire holders?

 

Some new information...

I saw some residue on the driver side exhaust manifold so I removed it to inspect it. I found the bolts near the #7 cylinder were loose causing an exhaust leak.

The threads for the #2 spark plug were damaged so I removed the passenger side manifold also and found the rear bolts on that side were loose also.

It looks like the lean condition may be caused by an exhaust leak from both manifolds as well as arcing from the wires/plugs.

I order Taylor wires and I bought Bosch Platinum 4 plugs.

I will be reinstalling everything over the next couple days and I'll update you with how it all works.