what state do you live in? the shop i use to work at would charge you maybe 5k for a reman. jasper engine installed. i would pull it and take it to a engine shop for an overhaul though it i was you. probably on the high end 3k for a full rebuild for that motor

 

Do not pay $16,000 for this job. When I traveled too Norfolk Assembly I would watch the mechanics (2) pull the cab and replace an engine in just over 3 hrs. Of course working with a hoist and a new truck makes things easier. There are really only like 6 large bolts holding the entire cab on the frame plus some linkage and harness connections.. I also have suspicions if you really need a new engine. If a piece of broken sparkplug or anything stuck in one of the valves holding it open then you would get low compression and would not need a new engine to repair it unless a lot of damage incurred. Sometimes the debris will fall out of the valve by itself and blow out with no ill effects. I doubt that the piston is broken. If it is you will have a lot of raw gas in the oil as the injector will still be spraying gas only now right into the crank case. Fifty percent loss of compression sounds like a valve may be stuck open. I always used to take compression several times if one cyl is low as well as change the gauge hose just to be sure it is not an equipment issue. A good mechanic would use a Borescope (fiberoptic camera) placed into the sparkplug hole so he could inspect the top of the piston, the bore and the valves and combustion chamber for damage. It also could very well be a valve train issue ( lash adjuster,follower, bent valve stem etc.) and the dealer didn't know what he was looking for....I know one thing I would replace engines all day everyday for that kind of money. Take this truck elsewhere for a different opinion even a good non Ford mechanic if you know of one. You should be able to either fix this engine or worst case have it replaced for a third of what they want to do it. Good luck

 

If in fact you are telling the truth I would get a legitimate quote for having a re manufactured 5.4 installed in your vehicle. I would then fax a copy of said $16,000 repair bill to you local news stations and the BBB.
I would then get quotes from various local shops and take them with you back to the stealership and demand to speak with the OWNER/MANAGER of the stealership.
I think the professionals on this site would agree that unless you are a certified mechanic possessing the tools required for said job, your best bet is to have a re manufactured 5.4 installed by a local mechanic. If you have something else to drive then you could do the swap your self. You can get on a "Waiting list" at your local scrap yards and attempt to get a motor from a wreck.
We can empathize with your frustration at the outrageous "Estimate" given to you and rest assured the majority of us here would have no problem telling that stealership in particular where to stick it.

 

Hey mitch,
yeah,,iv been a member her for a little wile.lol
I'm a member of a lot of Ford sites. This is one of the better ones!!!!

Phil