You might check your parts prices at Napa just to see what they would cost, belts,plugs,tranny filter and about 8 qts of tranny fluid. Add 40% to that number and your pretty close to what he is charging for parts. Having never worked on one I'm figuring he's about 450 to 550 high. Did he quote you a shop labor rate? When they clean injectors they hook a hose to a fitting on fuel rail attach a can of cleaner and let her run. Haven't priced that cleaner in a long time.

Have you ever changed the belts?
First thing I would do is go to auto zone and get me a can of SeaFoam or a bottle of Lucas fuel addative/ injector cleaner and run it through the engine and see if the hesitation goes away.