Grind them or bend them wheelin. As far as how much to leave, my personal prefference is about 1/4 inch past the nut. You should replace them every time you take them apart because they tend to stretch. Also make sure you tighten them again after about 500 miles or so.
Those skid plates only help if you've got a somewhat level plane under 'em. Any excess "screwage" through the skid plate and poking out the bottom would make them null. Chop 'em/grind 'em. Then consider the skid plates. Just make sure you've got enough threads to put 'em on.