I have a 2012 E350 Coupe and owned it for about 5 years now. It's got roughly 130K miles on it and it started doing this clacking/tapping sound (best i can describe) when I start the car up after it's sat over night or after its setup a long period of time.
Was curious if anyone else has had this issue, I had the check engine light to come on, but it went off so I'm not sure if it's something to be super concerned about. I know if I take it to the dealership it could be an arm and a leg for diagnosis but I may not have a choice. Any input would be greatly appreciated.

 

I would suggest checking this symptom immediately. Either with a dealer or a reputable indy shop. If you think the bill would be big now imagine the consequences if you let it go. With 130K on the clock it could be anything but most likely the top end of the motor. Good luck.

 

If engine # is below 30 567600 could be crank assembly per attached bulletin. Compare sound attachment. If engine # is not known post VIN I will confirm if included.

 

I had the exact same problem in my 2013 E350 Cab. It was the timing chain tensioner and was a pretty major repair. Luckily it was covered under warranty.

 

When hydraulic chain tensioners get old, they can lose their prime when sitting and are loose on engine starts and let the timing chain sling around until they pump up. The older the car gets the longer it takes for them to pump up since the oil pump gets worn too. They will need to be replaced.

Another possibility is worn hydraulic tappets which will need to be replaced as well. There are no cheap solutions to this problem. A temporary fix is to get a viscosity index improver and add it to the oil. This will work for awhile. This is a tried and true move at used car shops.

A short story I have is when I had a new Ford Probe GT with the all alloy 4 cam V6, the dealer consistently overfilled the oil by two quarts without my knowledge at every visit. The high oil level got whipped up by the crank hitting it and foamed it. Foamed oil does not pump well so I started having low oil pressure on trips and by the time I noticed and got it into the shop the valvetrain was destroyed. This was a new car! It cost them a ton to replace the motor! The symptoms of this failure were loud clacking on cold starts.