Some dogs with separation anxiety will have accidents almost immediately after the owner leaves..so I'm wondering if that's what's happening with your pup. The kong filled with treats/peanut butter might distract him long enough to get him past the initial panic (usually the worst behavior is within the first half hour). Try to keep leaving and coming home fairly low key...don't make a big deal out of it. I might try not scolding the pup for the accidents as that might be stressing him out as well. Zumie gave excellent advice on how to create a positive association with crating for your pup.
As to the mouthing, here's a site that offers lots of suggestions:
Got Puppy Nipping? Take the Clicker Approach | Karen Pryor Clickertraining