Plugs and COPs are are an easy DIY job unless you got the couple years with the defective plugs that break apart (07-08 afair).
Most "tuneup" services these days do NOT include COPs.
DIY cost plugs: $8 / plug genuine Motorcraft (Made in Japan) + $10-20 for a good spark plug removal socket with rubber insert helps... assuming you have a ratchet, swivel elbow, and extension already
DIY cost COPs:
$30-60 per set generic, depends on year
$300 per set genuine --- which clues you in that NO it is NOT included in the dealership service lol
Plugs and COPs are a 2 hour job going slow and careful with no prior experience... 30-40 minutes if you do en in one go and dont double check your work by restarting truck inbetween to check that each one was installed correctly.
COPs done later without plugs is a 10 minute job.
Air filter is like 8 or 10 bucks and just pops right in. Add a few minutes to take off the intake clean any crud inside and give the MAF a spray of MAF cleaner
Throttle body --- not a CBU prone engine, takes but a moment with the intake off.
Thermostat: it's like $8 do it while the intake is off it's right underneath. Cheaper to do it than to let it give you problems later.
Hoses:
Heater hoses are 40 bucks or so a pop online, $90 ea at dealership --- so that's not included either lol
Coolant flush:
Doubt they'd backflush it properly for that money, probably just wash out your radiator and overflow tank and add 2 gallons (leaving more than half untouched).... DIY its easy but a pain in the ass to do. Best done right before plugs and coils because accidental coolant/flush water spills into spark plug wells can mess up your COPs.
For proper DIY get a short piece of hose, get a flush tee, undo the heater hose where it goes into the engine and put the tee there with the short piece on the other side going to the block. Dont cut your heater hose unless youre planning to replace it right after the flush, those tees are NOT a quality product that'll last if left on.
Flush cost DIY:
Several bucks for a tee kit
$50ish on new coolant, Zerex G-05 or Motorcraft Gold (concentrate not prediluted)
Several bucks on distilled water.
Conclusion: Spend $150-200 and do it right yourself. If you risk generic coils, save your old ones in your garage and toss one or two of em in your trunk just in case...or just dont do them at all, since the dealership clearly wasnt planning to either
PS outside of the famous "coolant in spark plugs wells" mistake, its a Ford so your chances of breaking anything DiYing this are miniscule to nonexistent...unless you got the version with the defective plugs that break apart.