Did the lights go on in succession at the proper times after you lit the fire? Or did they go on at the same time as soon as you turned on the stove? The manual that Tj listed says that the thermocouple wires have to be connected specifically in the junction box. Yellow-positive to top center terminal, and Red-negative to lower center terminal. Is it possible they got reversed? I am not sure if that would cause a false voltage to be sent to the controller, preventing the igniter from going or not. I would definitely verify again that all your connections are correct in the junction box after you were working in there. As suggested earlier, did you check continuity for the igniter all the way to the controller and not just the harness? Did you figure out where those wires by the auger come from. Maybe someone replaced the auger motor using a new pigtail and those are just old ones, but you still need to check whats connected to them. To test for voltage to the auger motor I would just back probe the feed wire at the motor with your voltmeter and the other lead connected to chassis ground. Turn on the stove and see if you get voltage for a minute or two and then if it goes off, this will verify the controller is sending voltage for the initial feed for start up. Verify if the motor is running or not to make sure it's not just stripped gears or a loose locking collar.