Some of the things that will affect the health of the shell are basking temperatures and water quality. Do not be afraid to use a warm basking spot as this will facilitate shedding. I am currently using basking temperatures of 100 degrees. Make sure his water is very clean, as you can imagine this cannot be emphasized enough. What kind of filtration are you using, do you have gravel in the tank (get rid of it!), and do you do any water chemistry testing?
My personal feeling is to do some basic treatments at home before taking it to a vet. You could give him a mandatory dry out time, simply put him in a plastic container with the basking spot to keep them warm and dry. During this time you can apply some triple antibiotic (just generic stuff with no additives). During this time perhaps you could work on getting your turtle a little bit more used to handling?
By the way, I am the one who referred you here from the list serve.
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