OK, let's go over a few things.
First of all, you're paying for parts from their sources and then labor costs. If it's a dealership, then you're paying for factory original Ford parts, which is going to cost more than the parts store down the street. If it's a brake shop, you'll be paying whatever they pay for the parts from whatever store they get them from. Labor is based on how many hours the books say a certified mechanic SHOULD be able to do the job it. If the books say it takes 5 hours, you get charged for 5 hours...even if their guy is a whiz at F150 trucks and can do it in 2 hours.
Break pads/shoes will last about 50,000 miles, give or take depending on what pads/shoes you got and highway vs town mileage. So it's not unreasonable for your truck to need pads, depending on when this was last done.
Rotors are not unreasonable for a 2003 anything, especially if they've never been replaced. With 125,000 miles, it would not be unreasonable to need new rotors if they've never been replaced. The question here is whether there is enough metal on them to allow them to be turned, or if they're warped. It's a tradeoff here on cost of replacement vs cost and time to turn rotors, if they're turnable. Turning a rotor will run you about $15 to $25 per rotor, plus the time and transportation to take them to a shop to have them turned. Also, in my experience if you've got a warped rotor, just replace it even if there is plenty metal left to turn it. This is because a warped rotor WILL warp again after turning, because the warpage will result in uneven metal thickness on the rotor when it's turned. It doesn't mean it'll fail...just that it'll warp again, and likely sooner than it did before. It's a nuisance.
Calipers: I find it difficult to believe that ALL your calipers need replacing. But you need to inspect them to be sure. After about 10 years, it's not unreasonable to find that a caliper may need replacing. Look for degradation of the rubber piston boots and uneven wear of your brake pads (inside vs outside on each wheel). If the boots are rotted/damaged, replace the calipers. If you've got uneven wear of break pads, likely the caliper itself isn't bad but it may not be "floating" on its bolts/sleeves properly, which could mean it needs to be replaced. Also, does the truck pull to left or right when you brake? This could be due to several issues, among them being a caliper that doesn't squeeze down properly when you apply the brakes or release properly afterwards.
Flush: This is about a $100 job, if you pay someone for this. But you can do this yourself (preferably with a partner to make it easy) when you bleed your brake lines after a brake job. Start with replacing all the brake fluid in your master cylinder reservoir with new brake fluid. Then bleed each brake line as you would normally to get the air out, except keep doing it until you see the clean, new brake fluid come out. Keep an eye on your fluid level as you do this and top off as required to be sure you don't suck your reservoir dry and introduce air into the system. That's it.
Now, material cost. The internet is awesome here. Not knowing the full details necessary to look up your exact parts, I went to AutoZone's website and plugged in a random 2003 F150 and looked up some prices:
Rotors: About $50 each, give or take. Call it $200.
Pads: About $40 per set, give or take. Call it $80.
Calipers: About $60 each, give or take. Call it $240.
Brake fluid: About $8 a quart.
So you're looking at about $528 for parts, give or take, depending on what you need for your specific truck and what you choose among the various prices available. That's to do everything they want to do.
Looks like you've an offer or two here to have someone help you do the brake job, if you need. It's not difficult, really. Just take a little bit of time and some common tools. I'd take one of them up on the offer.
QUESTION: I'm not familiar with the F150 truck brake rotors. Are they JUST rotors, or are they rotors which require bearings? If they have bearings (like the rotors on my wife's old 2002 Explorer 4WD), then you'll need to either buy new bearings and grease to install in your new rotors, or remove the old bearings, clean and inspect them to be sure they're not damaged or burnt, then repack them and install them in the new rotors.