I think getting your car back ASAP is the first priority. If it where me I would go to the shop ready to pick the car up, but before taking it I would have him go over those areas in question with him. Have him show you where and why those areas are problems. I would suggest taking pictures of the car, specifically those areas in question, while it's in his shop. Get a written quote for fixing them that includes a time estimate for completing the work. This type of documentation combined with any other you might have will be useful IF you do end up in court.
As for the storage fees....is there is a written contract stating the terms and conditions of this type of charge? If not I would find it hard to believe he could enforce those charges.
Last suggestion. Be the professional...always nice, polite and respectful. Complement him on the work that you do like and show interest for future business dealings.
Keep us informed! I know many of us will be watching to and hoping for a positive outcome.
