If it's constantly cycling, there's a connection issue somewhere, or the contact inside the rotary switch are not making a connection.
The motors are all dipped in a rubber coating from the factory - maybe you have an original un-opened motor? They all look pretty cruddy in there at this age.
The only "indexing" that needs to be done is if you removed the splined armature while the motor was out, and lost position. When the motor is reinstalled - move the headlights to the UP position. Once the motor itself has moved to the UP position, you can fasten the linkage to the drive spline with the light in the UP position. Test a few times to make sure it closes properly, tweak as necessary.
Someone talked about the motors losing sync somewhere - that's not electrically possible. The switch inside the motor is a position encoder that reports to the headlight module. If the lights move opposite each other, one of your linkages is attatched 180 degrees the wrong way. If the light keeps cycling, the module is sending an up/down command but not getting any feedback from the switch