How do I tell a 5.2 from a 5.9

The only thing that may affect your decision on the 5.9 Jeep is that the starter is on the passenger side. As far as the engine block goes, I don't know if there are any differences. The air hat and air box are located on the driver's side, right where the a-body battery tray is located. The driver's side exhaust manifold outlet is turned inward and the head pipe will probably interfere with the starter.

Be sure and get the kickdown cable, trans cable bracket, trans shift lever, PDC, PCM, and wiring harness.
I have two Dodge 5.2's and a 98 Grand Cherokee 5.9. Give me a shout if you have any specific questions.