I don't believe it's Velvet

That shows up as golden to rusty coloured flakes covering the skin. I'm not convinced it is Gas Bubble Disease as I first thought either, given what you said about the lumps being white not translucent. It could be a fungus of some kind, mabye the injury early in life has left an area that is more susceptible to fungal infections than usual.
Treatment depends on whether you want to use meds or go natural. Malachite Green is the most common medication used for fungus or a Pimafix/Melafix combination if you want to go natural.
It could also be the start of Lymphocystis

Do you know if he's been exposed to other fish with Lympho at any point before you got him?