I have a couple suggestions for you, based on the options I ordered or didn't order on my 2013 F350 diesel dually 4x4 crewcab longbed. I fulltime so your mileage may vary.
1. If you have any thoughts of getting a 5er at some point, then I suggest that you get the Ford 5er prep package. In addition to the predrilled holes in the bed, it includes an additional umbilical electrical plugin in the bed - now you will have a total of two to choose from. You will get a set of plastic pucks to cover the holes if there is no hitch installed.
2. I got the Ford spray in bed liner. It seems to be a quality product and has held up well. Part of my thinking was that Ford would do all the prep work and would make sure the spray would coat all the edges of the holes that were cut as part of the 5er prep package. I have never run any kind of bed mat in my trucks. What happens when you get water trapped under it ???? RUST !
3. I did not get the dual alternator package and have not missed it. I have the Platinum model with diesel glow plugs, heated seats, running lights, etc and no problems. I believe the diesel option gets you a larger alternator then comes standard on a gas truck.
4. I agree that the Fx4 package is a joke. Check out what's really included in the package. I didn't want the crappy shocks from the package so I just ordered the skid plates separately (cheap)and put Bilstein 5100s on the truck right after I took delivery. Guess I'll have to live without the big decal that tells the world I drive a 4x4 truck.
5. I have the 3.73 rear end but that was the only one offered with my setup. I tow 14,000 pounds (gross) and all I can say is that towing is a dream. I would never want a lower (numerically) gear ratio. The gear selector never moves out of 'D'. This thing is a beast and doesn't seem to care how high the mountains are. I'm turning about 1600-1700 RPMs (maximum torque) at about 58-60 mph. And I can still get over 20 mpg on the highway when not towing.
6. I also got the optional upfitter switches. It's a cheap option ($125 ??) and will be handy if you want to wire up additional lighting, or maybe a fuel transfer pump when you get that auxiliary fuel tank in the bed (see my note below).
* Something to remember is that you get a significantly larger diesel fuel tank with an F350 longbed truck. I believe the tank is 26 gallons on a short bed truck and 37.5 on a longbed.
Tim