Oh no, poor Scoobs! Sounds like your sweetie has been through a lot. *scritchies* from me!!
My first guess would be mange. In order to diagnose this you will need to have a skin scraping done at the vet.
Mange is in no way a reflection of your care as an owner. Nor is it like a lot of other parasites (i.e. fleas, ticks, tapeworms) in that contact/ingestion/etc. is all that is needed to contract it. Demodectic mange (or 'demo') is fairly ubiquitous in the environment and whether or not a dog is affected has to do with their individual immune system. I think you will agree that your dog has been through a lot and probably has a somewhat compromised immune system.
This Fosters Smith page explains it well : http://www.peteducation.com/article....&articleid=729 .

Unfortunately the treatment for mange is not particularly cheap and generally many rechecks and skin scrapings are involved. Of course, these spots could also be due to something else- an allergic reaction, exposure to chemicals, etc. I would expect that were it related to allergies then you would see a marked decrease in inflammation after administering Benadryl. Did you notice if his skin 'calmed down' after you gave him the meds?
A vet would probably only consider the possibility of chemical burns after mange had been ruled out. At my vet office the most common types of chemical burns we see are from reactions to OTC flea/tick topicals or occasionally even the brands we dispense. Have you used any new topical products on him recently? I hope your neighbor would not be so hateful as to purposefully harm your pets. You might want to consider any chemicals he could have been exposed to whether in your yard/house or in other public places he frequents.

Anyway, I hope some of this proves helpful. I wish you and Scooby the very best. He sounds like a sweetie pie and I know you are worried. Let me know if you have any more questions, okay?

{{{HUGS}}}
Kate