I would make sure the temp of the water is just right, too warm or too cold are the only time I've seen a snake freak from water. You want to try to match his temp so its not shocking. This is probably cooler than what you would think. If it feels warm to the touch, its too warm for him. Hold him for a bit to let him get to your temp and then fill a small tub with approximately an inch of water at about your temp so to the touch you shouldn't feel a temp change. He shouldn't be submerged just like what sully said, you want him to be able to lay in there relaxed without having to worry about going under. Slowly lower him in and let him crawl in on his own. Then just cap it as long as you have a couple holes to vent. Put it in his enclosure so the temp stays ok. I've even left them in overnight but I'm not sure if that's a good idea, you may just want to leave him a couple hours so you can supervise. It has always worked like a charm for me getting them a nice easy shed. Look to improve the humidity in your enclosure and you should never need to do it again. It almost always happens to me when I get a new snake but once they are kept in high humidity they never seem to have a problem again.

As for him being skittish, that's very normal for a snake that hasn't been handled much. It's nothing to be worried about and doesn't necessarily mean he was abused, just that he's not used to being handled and is naturally scared. Normally you would want to leave him alone for a few weeks to let him get settled in to his new home before handling him too much because it adds to the stress but since you've already had him for 4 weeks your fine to start handling him on a regular basis. You just want to get him used to it so he wont be scared. I would try for maybe 10-15 minutes every day except for feeding day and a day or two after. Try not to go too much longer than this until he seems to be more calm. I've had some pretty nasty aggressive snakes, even wild caughts, that over time became very nice calm pets. Try to make the handling as stress free as possible. Quiet dim room, very slow movement and gentle non restrictive holding all help to keep them comfortable. Once they get used to being handled most don't have a care in the world about being handled and some even seem to enjoy it. Patients and consistency can turn him around. Just keep at it, and I'm sure he'll come around a lot quicker than you think. Good luck with him.