Personally I would eliminate the stock VGT while the engine is out. If you want to keep it simple I would do the EGR delete, PCV reroute, headstuds (depending on future plans), and an LML drivers side manifold (if you don't plan to put aftermarket ones on it in the future).
Just based on mileage of the engine, the water pump should be good for a long while. I don't know about the hit it might have taken from the front end impact.