best thing about wrecking yards is that for the rig to get wrecked, it had to be running down the road beforehand, which means unless the parts got mashed in the wreck, you are pretty safe to assume they will work once you get'em.
That said, as was stated before, you'll need the T-case off your donor rig. The bonus about going to a wrecking yard is that you can also get the wiring harness (for the neutral safety switch and reverse lights) the t-case linkage and shift (unless you are ESOF) the manual tranny shifter, boot, etc. Also, don't be cheap. Buy a new clutch release arm & pivot block for $35, a new flywheel and clutch setup, with kevlar pilot bearing, etc.
Oh, you will also need to get the tranny cooler and lines off the donor, also, along with cross-members, etc. THis is why I think you should go to a wrecker and find a donor. All this stuff will be hard to find and EXPENSIVE otherwise...
(Yes, the 6-spd ZF manual DOES have a cooler. There is a pump that is run anytime the clutch is engaged and the engine is running to circulate oil.)
Oh, and you can also get the clutch pedal assembly, brackets, and the new steering column cover to replace the one for your auto. Buy a new pre-bled master/slave kit from ford ($132) you'll thank me later... You literally cannot bleed the old unit once it ges air in it. Don't know why, but it really sucks...
Anyway, you get the picture. Going to a wrecking yard will allow you to find all these parts in one trip, instead of paying a fortune for the new parts one at a time...