Your setup is lovely. You've made quite an effort to make a great turtle home - I'm impressed.
I'm afraid your turtle's skin condition is pretty severe. The best thing would be to get prescription treatment from a vet. Try calling around and see if one would be willing to help. If there isn't one close by, at least maybe you can find one that will give you a prescription. If they need to see what's going on, you can email them the photos you've showed us.
If you absolutely can't find a vet that can help, here's some advice on treating skin problems from another well respected turtle site. Scroll down on the link until you find skin infections. Since your turtle's is pretty advanced, it may not be sufficient, but maybe it will. Acriflavin, the medication recommended on here, is a fish medication and around here we can get it at pet stores that sell fish.
http://www.austinsturtlepage.com/Care/medshell.htm
Do you have the ability to check the ph of your water? Ph that's too high (acidic) encourages the growth of fungus, and ph that's too low (basic) encourages bacteria. The recommendation in the link assumes the problem is fungal since it's advising that you lower the ph. Of course, if the infection is really bacterial, then lowering ph would not be a good idea, so it would be very helpful if you could find a vet to tell you which type of infection it is.