1. Should I strip him back to the bare lead as I don't usually paint over a black undercoat?
I would strip him down and give him a good cleaning - nice model BTW!
2. Should I try and get hold of a left hand (anyone have a spare?) or attempt to 'move' the thumb over to the correct side of the hand?
You could move the thumb over which should not be a big problem with some green stuff or as one already suggested have someone sculpt you a hand or a hook
3. Should he have a fully scenic base or leave the bare wood plinth?
I would mount him on a game base with the proper scenics so he can get back into action where he was meant to be.
4. Should he be dismantled and checked for internal pinning?
Again, i like to build/paint my own models so he would get totally stripped and then carefully rebuilt - but I am crazy nike that
good luck, I bet you have fun with this gold mine of a find.