I guess I would trust the machinist and his experience with these engines, but .002" doesn't seem to be a game ender to me.

The FSM spec for standard bore oil clearance is .002-.0035", so while the .002" looks like it would cause a spot with no lubrication, but since the engine has already been running in that condition, the truth is in what the bores look like. Do you see discoloration from heat? If not, they'll probably run ok unless there is a similar warp in the head and you mill that away. The way I said that is probably confusing.

BUT - to be safe and in agreement with the machinist is wise - particularly if his overall warranty is riding on the choice. I'd look for a set of heads from a DIY junkyard. Buy a warranty on the heads so you can take them back for another set if the machinist doesn't like 'em. As mentioned, the Caravan/Town & Country/Voyager heads will work - as will Diamante SOHC heads. You'll need to swap in your cams.

Frank