IMO, the '89 Runner in LA is listed about $2k higher than it should be based on the pics and what is wrong with it.  I wouldn't even be able to make an offer since I would be below $2k with my initial one.  Even if every thing was working properly and no chips on the passenger side shell, I wouldn't go over $2500 tops with what the rest of the interior looked like.  With sellers like this, he is likely pricing it at what he needs to get to buy something else he is after, and not pricing it at what he really thinks it is worth.

FWIW, the clutch issue sounds like it is the slave cylinder, cheap fix yourself, but a couple of hundred at a shop.  The A/C could be anything from an electrical issue like a fuse or connector to a seized compressor, and the system would have been R12 from the factory, but could have a DIY R134 conversion kit on it.