I have a 5.2l Magnum in my CJ-8. Here is a couple links to a CJ forum where I posted pics of my CJ and answered a bunch of questions about the swap:
http://www.cjoffroad.com/forums/topic.asp?TOPIC_ID=17626&SearchTerms=5.2l,magnum
http://www.cjoffroad.com/forums/topic.asp?TOPIC_ID=18811&SearchTerms=5.2l,Magnum
I've posted alot over there about the swap so search around a bit more!
As for the conversion in the Pajaro, You would be best off using a '92-'95 OBD-1 setup as the EFI is simpler than the OBD-2, with less sensors. The wiring conversion is basically the same as swapping in a 4.0l using an original harness, except for the two extra injectors!
As for the trans, you will need to decide on what driveline length is acceptable. The '93-'95 used a 46RH automatic, which is hydraulicly controlled (except for the lockup and overdrive), but it's pretty long. The '96 and later models used the lighter duty 44RE which is electronically controlled by the OBD-2 PCM. If you run OBD-2, you can wire it all in with the engine harness. It's about 5" shorter, if I remember right. There's a chance that if you use a transmission controller from a '93-'95 ZJ 4.0l 42RE, you could use the 44RE with the OBD-1 system. One more auto Overdrive is the 46RE, from a Dakota, Durango or ZJ 5.9l. Basically it's the same length as the 44RE, with the main guts of the 727, but fully electronic.
If overdrive is not needed, a 727 can be used from a Dodge truck. With a Jeep Grand Wagoneer output shaft and rear adapter housing, the length is around 23.5" Non Magnum transmissions can be adapted by simply grinding in a hole to clear the block mounted crank sensor.
Four or Five speed Manual transmissions are an option too, but they only came out of Dodge trucks.
One more thing about the transmissions, Dodge transmissions have the starter on the left side, ZJ transmissions have the starter on the right side, tucked in a bit tighter for more clearance.
Hope this helps!
P.S. My stock 5.2l Magnum gets around 16 MPG in daily driving, and has ALOT more bottom end than my EFI 4.2l had, plus double the HP at around 220-230 stock.
P.P.S. If more torque is needed, the 5.9l Magnum will fit exactly the same and has around 50 lbs/ft more than the 295 that the 318 has. New 4" stroker cranks are relatively inexpensive at around $300 for cast ones good to around 500 HP, which will bring a 318 to a 390, and a 360 to a 408 using stock length rods and inexpensive pistons, the whole stroker doesn't cost much more than a normal rebuild!