I have bought a bunch of games from Rob & he is always great about pointing out stuff that he knows about the game, good and bad.
He does go through a ton of games (said getting 40 in this week in another thread) and stuff can fall through the cracks. $3200 from a retail operation shipped to your door sounds about right to me, if not low. Remember he is retail, overhead, brick & mortar and shipping isn't free.
It sounds like he is willing to work something out with the OP. Returning IMHO would be a hassle & the problems seem fixable and stuff that's handy to learn for pinball ownership. I'm sure there is a cash middle ground that would make everyone happy...