Do the ground voltage checks when you dump the codes. The first thing that happens with a code dump is that the computer toggles all the relays, solenoids and actuators. If you miss it the first time, remove the test jumper and do it again.
Update -
The car finally has the correct CATs with a functioning secondary air injection system going to them. New O2 sensors, spark plugs, cap and rotor, oil and filter. There are no identifiable vacuum leaks and it passes all the tests I have thrown at it with the exception of the 44 and 94 codes. I got a tip from another forum to check for clogged air passages in the head to loosen the crossover pipe (which I removed and cleared previously) and start the engine and listen to see if exhaust gasses were coming from the loosened area of the crossover pipe. I got nothing so my conclusion is that the heads are blocked and that is what is setting the codes. It always passes the cylinder balance tests and no other codes have been set.
I did make sure that the air pump and valves are working correctly. If I may make a suggestion for anyone have problems in this area is to simply test the functionality of the air injection system. Just disconnect the hoses leading to the crossover and the CATs at the pipes. Start the car cold and check to see if air is coming from the hose that was connected to the crossover pipe. If yes, it's working cold. Now let the engine fully warm up and checking the hose going to the CATs, bring the RPM up and check to see if air is coming from that hose and none coming from the other hose. If it passes this simple test then you have effectively checked the entire air injection system from the air pump to the diverter valves including the two solenoids. If it doesn't pass, then it's time to check individual components. Please correct me if my conclusion in wrong.
I took the Mustang to be emissioned after all that and it failed again for the same, high HC. However, the reading was much lower, 3.74 ppm vs. 9.47 ppm (previously). The limit is 2.50 ppm. The spikes in the HC occur at around 20-25 mph then settle lower but not low enough for the average reading. Interestingly, the CO spikes a bit at the same time but drops quickly. This is a dynamometer test and its run twice with the same result both times. The HC stays highest as the car is slowly decelerating down to idle and doesn't return to near 0 until the car has been idling for a few seconds.
At this point I don't know what else to do. I am suspicious of the ECM in that it might be causing the high emissions some how. Sometimes the car will be idling normally around 850 and will suddenly idle up to 1500. The only way I can bring it back down is to shut if off for a minute.
Anyone got any TNT? HELP!