First thing you need to do is pop the battery out of the CLC card, with power on. It's a BR2430. It should be over 3.0 vdc. If it's less than that replace it with a new battery. That's what stores the shaft learns, parameters, etc in the volatile memory.
No sense in going through all the setups if you can loose them if the power goes out.

It's pretty quick and easy to do a shaft learn on the dmc. Sit on the cartop with your laptop plugged into the door operators com plug and you can do it all from there.

One thing I've seen mess with door learns not taking or seting up right is loose hardware on the operator linkages. I'd put a wrench on all the bolts real quick to be sure.

I do find it a little odd it wants a shaft learn to do a door setup, mainly because it sounds like these cars are running currently and it wouldn't be running without a valid shaft setup saved. I'm not the most familiar with Worlds freedom tool, I've used it once or twice but normally use DMC Fast on a laptop. Have you called world to ask them? They should support their product with a little support for using it.