You will have to readjust the box if you pull the side cover off. The new gasket thickness is enough to change the adjustment. Your better off pulling the box out and doing a proper cleaning and adjusting. They are not hard to work on, and with the engine out, not all that hard to get out of the truck. Better now that you have time.

https://www.flickr.com/photos/advance-design_parts_co/sets/72157632210242370/