Magnum swaps are fairly straight-forward... here are some answers off the top of my head:
- ZJ motor (except for 1998) will be a 5.2L. In my experience with Magnums (which includes a few swaps and a recent stroker build), you can usually find a 5.9L from a Ram 1500/2500 much easier and cheaper. The Ram P/S is taller than the ZJ, but that is a relatively easier swap and ZJ take-off parts are readily available. ZJ (except the 'Niner) has return-style fuel rail. The 96+ Ram Magnums are returnless style and will work perfectly with your 2002 TJ fuel system.
- To get an ECM that will work with your gauges and dash, IIRC you'll need a 2001-2003 Ram ECM (which is PCI communication based). Based on EPA requirements, you will need a 02-03 ECM to being fully compliant.
- You can use a Dakota bellhousing (must be from an AX-equipped Dakota with a 3.9L). You will use a flywheel appropriate for your engine block, Jeep clutch and throwout bearing, Jeep pressure plate, and Ram/Magnum pilot bearing (note that there are a few early odd-year Magnums that need to be run with a pilot bearing and adapter).
- Wiring is really easy. The Magnum ECM only needs ~15 wires connected/spliced to get full functionality. If you do it right, your Connector C on a 3-plug JTEC ECM will work perfectly with the Magnum JTEC. There are some wires that will need to be spliced into the Connector B + A harness (the one that goes to the engine and trans) but that's straight forward (can't blanket statement what would need to be connected as there are a number of changes in the 98.5+ years, so it would depend on what you have).