Gregg,
I have over 20 of these units in different road names and I have found a couple of root causes that take some bit of work on your end. first flip the units over and verify they are made similar to each other. All F3 units around 2003 time frame had all axles geared and driven. Later releases in 2005 had only one axle powered. Note that you are not mixing the types together. I think 2005 releases where F-7's not F3s. Also the worm diameter off of the DC motor is different between these years as well so MUing them together will not work.
Next inspect the trucks for any metal foreign matter getting into the gears. These earlier units had magni-traction and are prone to picking up metal particles and jamming up the gears in the trucks. cleaning these trucks out of all grease and hair is not for the faint of heart either.
If you are still convinced that these are similar makes with similar gears and worms. Lionel had a rash of problems with the earlier release of F3's with TMCC motors. I have pin pointed it to the motor bushings... if you pop the shell off you will see one motor working harder than the other appears to bind. I have traced it to the actual motor binding in the housing.
I tried GENTLY tapping on the shaft to seat the motor in its bushing and noticed that it works for all about one lap around the layout. if you pull the motor out you can also feel it has high friction forces as you try to spin it.
Worse part of this is Lionel does not have parts for the sensor board assembly with flywheel with the proper worm diameter. You have to either pull the worm off the old and place on the new part number or build one from a dummy motor with the proper worm motor already installed.