I'm in the same boat. My 99 5.4 4x4 needs a new transmission but it make no financial sense to have it rebuilt. I've considered the junkyard option but I'm a firm believer in you get what you pay for. So it sits until I either sell it, rebuild it myself, or get lucky and find something that'll swap in...
That idea doesn't hold much truth to junkyard parts. Most Parts on a vehicle and the salvage yard are perfectly good. There is an occasion where a vehicle is junk because of the engine or the transmission but a vast majority are junk because they are in an accident.
If the junkyard does not note the mileage it is hard to tell that even Because unless you take a battery and have the key in the ignition you can't see the odometer reading. Some are more willing to work with you than others and others know the mileage when the vehicles are brought in. I would have no problems purchasing a transmission for my vehicle if it looked to be in decent shape without excessive wear inside on the seat and the pedals Etc and was hit in the side or the rear or even a front-end or Fender Collision. The odds are greatly in your favor that the transmission will be just fine.
They warranty them anyways but of course who wants to install one that's bad and have to reinstall the next one. BUT for the price difference involved that would still even be a good deal having to install one twice. I will take my chances with used.
Another decent option is to pull the transmission and go find you a transmission shop or someone that's willing to rebuild it for you.
Have it in the back of your truck and go by a transmission shop close to closing or right after or on the weekend and pull around to the shop area and start talking to someone. You'd be surprised what kind of deals you you can get that way.
Or just stop by and go to the shop area and look for the guy who's building them on the table and ask him if he has any time to build one on the side.
Many of these guys will hook you up for a very good price and they make a pretty penny to but you save a ton.
