By cheap does he mean scanners in the $100 - $300 price range? I think you need a NEW mechanic. The lower priced do-it-yourself scanners perform READ functions with the engine controller. About the only WRITE function to the engine controller they perform is to clear codes. The accusation is unfounded.I have a scanner but my mechanic says that those cheap scanners can screw things up.
I think you need to resolve the misfire conditions. Did you check the spark plugs to make sure they are clean, properly gapped and center electrode not corroded? With only 73000 miles on the clock this vehicle has sat unused for extended time periods so you may have one or more fuel injectors that are not spraying fuel correctly. They might need to be removed and cleaned thoroughly.