Regarding the $250 for the water pump replacement; I would think most mechanics would know to recommend changing the water pump WTIT (while they're in there) if an engine has that type of configuration and would charge accordingly, but whether a service-writing program automatically adjusts for a timing-belt/water pump job is debatable.

That same labor charge showed up twice when I was inquiring about having the timing belt/water pump job done on one of my vehicles at a Ford dealer once. When I asked why it was listed that way when I knew that once the timing belt job was halfway completed, only seven more bolts would have to be removed to install the water pump, I was told that the total was just an estimate and would be adjusted later. Whether that would have happened is also debatable, but it made me suspicious enough that I didn't hang around to find out. (I ended up buying the parts and doing the work myself).

Since the VX is no longer at the first shop, you may be able to get the additional charge (and any other issues) sorted out by going through your local Better Business Bureau before resorting to a lawsuit. The BBB route is more democratic and less likely to put anyone into total defensive mode. The first shop may be inclined to work with you to prevent getting a black mark added to their BBB listing, especially if you can get the Isuzu dealer to corroborate any unnecessary charge(s) or questionable work.