2006 LJ, if I remember correctly the pcm will come from the dealer blank. Then the dealer will install and program the software you need with your VIN.
A lot of independent shops subscribe to a service from companies like Snap-On and are able to do this also.
If buy Pcm from one of the many aftermarket suppliers then they will send it to you programed.
A used Pcm will have the software from whatever it came out of and the dealer can only update that software. So if you have a auto and the used is from a manual they cannot change it to suit your needs.
Now it gets confusing with sentry key (grey keys) and vehicle theft (VTSS). If equipped a used pcm will have that information from the donor vehicle and not work. Sometimes a dealer can rewrite a VIN and program your keys to get it to work but not always. So a used pcm is one of those buyer beware sort of things.
2014 JKU, JKS lift,Poison spyder flares, bombshell covers,Rancho D2 control arms, JKS adjustable track bars, 35" Tires. GrabBars, Crawler Conceptz rear bumper, Smitty front bumper, Winch. Rough Country inner fenders, Teraflex Disco Mud Flaps
Backseat Dobermann Security