Sounds like you guys are on the right track! Do you know what the scabs are from? Could they be from being in a cement kennel at the shelter? How good were they about cleaning up after the animals? I know sometimes they can get urine burns if they're laying in it for too long (any time is too long, but it's a little hard to keep up with in a kennel).
Are you crating him at home? If so, are their blankets in the crate? We made the mistake of crating our foster (has been adopted) with blankets and she would root in them so much and move them around she rubbed the top of her nose raw. Could it be something like that?
I'd just wash him with the shampoo and keep everything as clean as you can (and not let him lick his wounds), and put the vasoline on the nose-since it's dry. I don't know if I'd put it on the scab on his ankle. In my mind in order for something like that to heal it has to be able to breathe and covering it with vasoline would prevent that. Since his nose is lacking moisture, it makes sense to me to put the vasoline there.
But I could be wrong.
Good luck, be sure to post pictures some time!