DON'T GIVE HIM A DIME BACK! I had a garage business for over 10 years and there is no way it would cost more than a couple hundred dollars to fix back up lights. As far as rear window leaking - I didn't look at your pictures closely but if it has sliding rear window they always leak a little if you pressure wash a vehicle or something like that. If they are leaking from just rain it is likely the little drain holes in the tracks just have some dirt in them and would be a 10 minute fix. Hell a new window wouldn't cost more than a few hundred dollars. GUY IS JUST TRYING FOR A BACK END DISCOUNT.
As far as tags - report them stolen and be done with it. Just go to State Police Barracks - tell them what happened (short story no need to get into all the BS). "Guy bought truck & used your plates to get it home - never mailed plates back to you - what should you do about stolen plates". They will advise you how to proceed. I am sure you are not the first person to have this happen!