im a neewbie to torts so really can't confidently or compantly offer any advice. i would hazzard a guess that as you have said past conditions have not been ideal and have lead to improper growth, (I think showing pyramiding?) . i would punch in a search into shell rot on here, should find pics, diagnosis, treatment etc. i think rot is caused by substrate being too moist at top layer, taking pyramiding into account i would think shell rot would not be a concern as are due to opposite extremes? given the pellet substate i would suggest daily soakes and changing to co co coir as soon as poss. PLEASE DONT TAKE ADVICE AS GOSPEL THOUGH!
As i say i am by no means an expert! you are in the right place, just keep posting pics and temps etc, you will be properly advised. i have leared that torts are tough little buggers! changes dont have to be made overnight, he/ahe will be thankfull you have rescued
The light places on his shell, from what I can see, are normal. Shell rot usually occurs on the plastron.