Fist off thank you for your service to the country.
The parts list would be the key to the price. Also did the mechanic pull the motor and is he putting it back in? Any head work to go along with it? Is he handling all the misc stuff like break in? Is he going to guarantee his work? If so then the price would seem in line.
Just some random thoughts. The windage tray that was missing is not 100% needed especially if the oil pan is baffled. The factory ones tend to crack. I have heard noting but good things about the aftermarket ones sold through Buttler.
The missing tube on the inside is also a common problem and most end up with the same issue you did. The dipstick gets broke off causing damage.
For myself I'm a big stickler on parts. I spend enough time on the PY board to know what parts are good and what to stay away from. It also depends greatly on the performance level your trying to achieve.