The step out warning light , might be a Monaco add on , controlled by a contact button touched by the mechanism ; when retracted; to turn it off .
Don't think it was a Kwikee option.
The motor is shut off by a load sensor in the control module , so if the motor ran at all while the linkage was disconnected , it may have stopped past the travel of the mechanism. Find the wiring connected to the motor , have some one close the door so the controller will start the retract cycle ; then disconnect the power from the motor as soon, as it moves the linkage. Then line up the step linkage.
Lube the mechanism , and run the steps through their cycle a number of times ; if the steps work properly ; then I'd say don't replace anything .
Very hard to fix something that's working the way it should.
Here are some files that may help. If you have trouble again.