John,
Not an expert on this but will try to help. Assuming cover is like mine, it is driven by a 12v actuated air cylinder located under the floor at the inboard side of the cover. Mine has an access door under the carpet but I think it is also accessible from underneath. My cover has stopped working a couple of time due to build-up in the channels the cover slides in, but normally it would slow down before stopping completely. Cleaning the channels with compressed air and spraying a bit of WD40 or silicone remedied the issue for me. If that isn't it, I would check to see if I had 12v at the cover switch. I think it's wired so that 12v is supplied to either the open or close side of the cylinder. If no voltage, there are a couple of 5A relays in the electrical bay labeled step. I'd guess that one of them supplies voltage to the cover while the other to the step. See if you have 12v at both. If thats all OK, I'd next check to see if the air cylinder is working.
Sorry I couldn't be more specific. Good Luck.
Steve