All the prices are fair. I am assuming they are ordering the Calmini 3" kit. Being a 4x4 shop I think they could part together a better kit. I see absolutely NO reason to even put the shocks included in the lift kit on your truck. They are really that bad, so why buy them. The Sway bar links are also a waste of $$$ because no one runs the sway bar and proper shocks will do some of the sway bar job anyway.
Have the shop look into buying the parts you really do need (Upper Control Arms, T-Bars, shackles, AAL or new leaf spring pack, and good shocks.) They/you can choose these parts from Calmini, Automotive Customizers, Spencer Low Racing, or Total Chaos.
The installation prices seem fair though I would suggest you look for someone in your area willing to help you do it yourself. That way you save money and learn about your truck. It really isn't rocket science.
One thing you will need and have ignored is some sort of steering upgrade. Running the bigger tires will kill the stock steering fast even with just a body lift and even faster with a suspension lift.