If you removed the wires from the limit switch assembly they go on this way. Yellow to the up contact. Gray to the center contact and Brown to the down contact.

And to get everything back into sync:

Make sure you put the black cup back on the end of the motor shaft and that it is pressed all the way on. Make sure the RPM sensor is plugged in. If neither of these are the issue, then you probably did not have the motor shaft pushed all the way back when you tightened the coupler after replacing the worm gear. Loosen that coupler up and from the front of the motor (opposite end in which the coupler is on) push the shaft back as far as it will go. Hold it there while you tighten the coupler back up and then try it.

Chunk the Craftsman garage door opener and buy a Genie. If you keep it you will be doing more research in the future to repair the thing over and over.