What could have I done?, Car is running on only 2 and 3. Options

[robkammer]

All: In prepping our BB for the vintage event next week I have done the following, along with a couple of fellow cult members. I had experienced a rather jolting banging at the right rear corner only in fifth gear. Between us, we diagnosed this as a transmission issue.
Pulled the tranny and took it to the good Doctor last week. He pulled it apart and found nothing major, only some minor wear items that he replaced.

Once back in the shop I looked more closely at the CV's.They were dry and binding badly. This was the problem. Ordered rebuilt's from George and installed them, when they FINALLY arrived.

All good, so we thought.

Got the axles in, wheels on, lowered the car and fired it up. Runs like , uh, crap.
Pulled the disty cap, Ok, new cap, rotor and points should do it. Nah.

Pulled plug wires 3#4, no change. It is running on 1#2 only.

Pulled #4 plug, beautiful. a nice shade of tan.

Put a timing light on all four plug wires, all are getting juice.

Called John at Air cooled Plus to see if there was any possibility that his flywheel work could be the cause. Nope.

He did grab a Bosch manual and alert us to a second set of contact points in the distributor, below the ignition points, that fire the injectors. Who knew?

Pulled the disty, cleaned the FI points, all good. Still running on 1&2.

Fellow cult member Jeff had a spare FI box and distributor, swapped boxes, no change. Pulled the FI points and tested continuity and they are performing just as the points in the car are, and also test the same.

Good continuity between the disty trigger contact and injector contacts on all four cylinders

Errlier, while I was waiting for parts, I did de-A/C the car. Pulled the condenser, receiver dryer, the underdash console and all of the hoses. Installed a correct tall console. I needed to pull some of the derelict wiring from the engine bay through the console to complete the process. I left the compressor in until I pull the engine this winter. It all went well without any drama.

At least I thought so

I can't think of anything in the passenger compartment that would affect the FI. We were only working in the back, pulling the transaxle and axle shafts. What could we possibly have touched to kill the two cylinders?

Any input would be welcome. At this point I'm relegated to taking another car to the event.

Cheers!
Rob

[Artfrombama]

Try a new ignition condenser.
Cheap and easy. A bad condenser will drive you crazy, will give a misfire not unlike you describe.