First thing we got to mention is your plan get the bed off the frame off once it is unbolted and unhooked. You either about four decently sized people to lift the bed or you need a two post lift. The two post lift is the safest choice, but I have heard of some people using other creative ideas like a hoist from some rafters. For the purposes of this article, I will be describing how to do it with a two post lift but the lifting it off route works just as well.
Bed Removal - 1999 to 2016 Superduty
A small amount of parts and tools you will need to remove your bed is required. You will likely need 8 new bed bolts and clips (f150 and f250 models only use 6) because the old ones will likely not be salvageable. Ford uses a box bolt called a TAPTITE2000. You can see a short video of a guy explaining these bolts HERE. In short, the bolts are blown down at the factory using a power tool into a clip attached to the frame that is not threaded. These bolts require the use of a size 50 torx PLUS socket (do NOT use a T47). Once the bolts and clips get rusty they are nearly impossible to remove. Most of the time you will shatter your torx plus socket or the caged nut will spin free. If you want expensive Ford replacement bolts, you will have to contact the dealer. Below, I have linked to the entire set of aftermarket replacement bolts and nuts.
W708770 & W714263-S900 (Ford P/N - sold each)
Ford SuperDuty Bed Bolt & Nut Kit
Torx Plus TP50 **Must be TORX PLUS not regular TORX**
Attempt to remove the bolts with a decent impact gun. If the bolt doesn't budge within the first second or so, you better stop trying otherwise you will shatter that torx plus socket. Go through and see if any bolts will come out. The remaining bolts you can try using a torch to heat the caged nuts. Most of them can be accessed from underneath. Otherwise, the easiest way to remove the remaining stubborn bolts is to grind the head off with an angle grinder. Be sure to point the sparks away from the rear glass!
Once you have removed or cut all the bed bolts, you can now roll under the truck and unplug the bed harness and bumper harness connectors. Also remove the three bolts attaching the fuel fill hose to the bed and position aside. On earlier model trucks, look for cables that are bolted to the truck frame that are wrapped around the bed frame. On brand new diesel trucks, you also need to remove the mount for the DEF fill. Now using your two post lift or your group of friends, lift the bed off the truck frame while being careful to clear the fuel fill hoses.
If you are removing the bed due to rust, you can repair the bed once it is off. The support rails (picture is wrong but right part!) can be purchased and even include new bed bolts.
Bed Replacement - 1999 to 2016 Superduty
You can also replace the truck bed with one from a newer truck (2016 and older). The beds are interchangeable with slight modifications from 1999 to 2016. Retrofitting a brand new bed to an older truck is simple but you will have to rewire the bed harness and drill new holes for the fuel filler assembly to mount to (or replace it with a new one). The connectors change several times between years. If you are adapting a 1999-2007 truck to a 2008-2014 bed, the cheapest way to rewire the bed harness is to cut off the old bed side harness, cut off the new bed side harness, and resplice the old bed harness to the new bed that's assuming your connector is in good shape. I have included a few wire diagrams by year.
1999-2001 F-series Bed Harness C401
2002-2004 F-Series Bed Harness C408 (same locations/colors as older C401, but uses a newer connector - old picture shown)
2005-2007 F-Series Bed Harness C408 (same connecter as 02-04, but has different pin numbering - same locations)
2008-2010 F-Series Bed Harness C496
2012-2013 F-Series Bed Harness
2014 F-series Bed Harness (same colors, same connector as 08-13, different pin locations)
I cant give an exact splice conversion chart, because pin locations and/or colors are different depending on the year of the truck and the year of bed you are installing. Print the correct diagrams (one for your truck and one of the new bed) above. Use the annotations I made in the diagrams and make easy match-ups regardless of wire color. The bumper harness (license plate lights) needs to be wired in separately to your connector by splicing into a "parking" wire and the "ground" wire.
A new long bed including tail lights and tailgate was running around $1700, whereas a short bed would cost you a smooth $2300. With the body style chance of the 2017 models, those new take off beds are getting rare and the prices may have skyrocketed. You should see how much better my Early 1999 With A New Bed looks. Get yours now!
Notes about the 2017 Superduty Bed
Unfortunately, the new Superduty beds in the 2017 model year and newer are not compatible for older framed trucks. The main difference is the bed mounting structure and frame design. The new SuperDuty frame, where the bed attaches, is not parallel to each other. It is wider at the front of the bed, gets narrower, and slightly widens again at the rear similar to an hourglass. In essence, the bolts are not in a straight line. Surely someone could drill some new holes and brace the box tubes where the new bolts go through, but that seems like a lot of work.
The bed bolts are now of a different design as well. A design I think is somewhat silly, as the rear most bolts are likely to get snagged if you are sliding in stuff to the box. The new bed bolts will require a new tool for you to own... an external torx socket - EP24. Slightly harder to get a hold of right now but it is available. Mostly left out of other "master kits".