Hiya Esch
1) If I have a building with lets say 100 prims, and I drag them all into a box and then have the box set to sell. Will the land that this single box is located on only charge me 1 prim or will it look at the contents and charge me 101 prims to have it there on the land? How does all that work?
If you drag the prefab into a box to sell, it will only be counted as 1 prim.
2) When someones buys this box, how will they get the building out in one piece? If it's all linked before entering the box, will it remember that when it drags everything out? Is there some sort of unpacking script that will do all the work for someone in case it doesn't drag everything out at once?
When someone buys the box they can right click the box then select edit, click the contents tab and drag it into the ineventory, Most people already know how to do this but you can type a notecard by opening inventory, up the very top click new, then note, type the instructions then place that notecard along with your prefab into the box, Yes there is a script I'm not sure what its called, You can type in scripts into find and alot of places that sells scripts will show up, Try hunting through all of them.
3) Also is it possible to do one large sweep of permission settings if all the pieces of the building are linked together, or do I have to set permissions for each piece individually before hand?
With prefabs I'm pretty sure once you link you can set the permissions, However if you set the prefab modifyable (Alot of people do prefer this) then a person can unlink you prefab and if you haven't set all pieces they may be able to copy the boards.
If you apply textures I would suggest setting permissions on those first. Once you apply them to an object those permissions automatically set on the prim.
4) Is there anything else I need to do or consider when packaging buildings for sale?
Take some good snapshots, People like to see what they are purchasing. When placing a description make sure to include everything the buyer should know.
You can type that up in a notecard aswell.
If I may make one more suggestion, It would be set the permissions on each object copy/mod/no transfer, This way if someone pulls the prefab out, decides to make some changes and doesn't like it, they can delete that one and pull another copy out.
That is just my suggestion, Not all prefab builders set those permissions, and it's up to you on wether you want to go that way

Good luck with your prefabs and I hope it all works out.
Nat