For your file problems, don't use the jig on the base edge, wrap a layer of tape on your file to raise it 1 degree and run that down your board cleaning it often to remove burs that get ground into the base and be sure to only go from tip to tail, not the other way. Also, it doesnt take much pressure to touch them up, too much and you will ruin your edges.
For your wax problem, are you pushing the scraper or are you draging it? If you are pushing it, it will hop and make grooves in your base. Keep your scraper flat by running it on a file along its length to keep your scraper true, if there is a void when you place your scraper on a straight edge, it needs to be reshaped.