I have LOTS of Dodge, Jeep and Chrysler parts manuals. Pretty much everything Daimler has released since the 80's. You are more than welcome to them all. Just drop me an email at info at alljeep dot com. They are all PDF's. In my experience, they don't change part numbers unless the item changes - not the application.
Now I'm looking at the 04 Jeep Wrangler, and there are 11 different PCM's for this year alone, or 6 for US emissions alone. 2 are for the Rubicon, so that leaves 4 for the other Wranglers. And I don't see where any of these transfer to any other rig, but the 04 Jeep Wrangler.
56044419AC - 56044419AD - 4.0L Manual Rubicon
56044421AC - 56044421AD - Export
56044422AC - 56044422AD - Export
56044433AC - 56044433AD - 4.0L Auto Rubicon
56044434AA - 56044434AB - Export
56044447AC - 56044447AD - Export
56044452AC - 56044452AD - Export
56044455AC - 56044455AD - 2.4L Manual Wrangler
56044473AC - 56044473AD - Export
56044474AC - 56044474AD - 2.4L Auto Wrangler
56044477AC - 56044477AD - 4.0L Manual Wrangler
56044478AC - 56044478AD - 4.0L Auto Wrangler
So it looks like the one year would have 6 different computers. Depending on weither it was auto or manual, or which motor it had or if it had Rubicon trim or not. The only difference that I know of between the 4.0 in the Rubicon and in the other Wranglers is the Rubicon is supposed to have about 20% more power than the others. I believe the PCM's will succesfully swap between them - as long as it was auto/auto and manual/manual.
...Anyway, sorry for the tangent