I see, so you're downtown. Heh, I'm on the east side of town.
Hmm, so Autozone sells the lower ball joint, not the upper one. My guess is that for the upper one, you have to change the whole thing out, which is why they are "including" the upper control arm. On Tascaparts.com, they sell the upper control arm for 211 and 179 (right and left). They list MSRP for 320 and 275 (right and left). To remove the upper control arm, you have to remove the spring/shock assembly, then loosen 3 bolts, which means you'd need to get a spring compressor big enough to compress the spring. I wonder if you can borrow that from Autozone.
For the lower, as mentioned earlier, you can get the ball joint at auto zone or advance auto, which makes it seem like you should be able to replace that without the control arm (which is why the quote for the lower is a lot cheaper.) The manual doesn't list a specific way of doing this, though.
As for the coils, you can get Global coils for like 80-90 for all 8 (I think these are the ones that everyone on F150online uses). The plugs, you can get at Autozone/Advance for like 5 each and do it all yourself. I could help you with that.
For the injector flush, you could try Gumout Regane Fuel System Cleaner. You can get it at walmart. Has to be the one with regane. Get the complete one, not the high mileage one.
Don't flash the PCM. If it's worked till now, it shouldn't need to be "flashed".
And as I said before, the filter should be easy.
I'll call my friend to see if he knows any good shops, though not sure if he'll get back to me right away. Also, have you done a visual inspection to see if anything is physically broken? Lift the front up and see if there's any play in the wheel.