Congrats on the new friend, he's a lucky guy to find you! The red scales are probably scale rot (from the unsanitary conditions you described) and something else you can do to help is use an antibiotic ointment on the red areas (like Neosporin) until the next shed. Try to work on the humdity in the tank vs. soaking him, because keeping those areas wet can make them worse. Retained shed (with the exception of eyecaps and tail tip) is more a cosmetic issue. Good luck!