The Magnum engine is still a very viable candidate and if I didn't find a Hemi/65RFE for super cheap and in great shape, I would have certainly went the built Magnum route. While they aren't the cheapest engines to make MAX POWAH!!, they are solid options for a wheeling rig. My RamCharger with a built Magnum stroker has scared plenty of people already and it isn't even tuned yet...
Anyways, back to your question. There were actually 3 different communication protocols in the TJ: 96-99 was CCD, 00-04 was PCI, and 05-06 was CANbus. The various Mopars you listed above also made the switch, but the years of the changes don't necessarily match up with the TJ (typical Dodge). I've done a few Magnum swaps (not into a Jeep though) and am fairly familiar with the different year Ram harnesses/ECMs since that is my go-to (they're easier to find!).
For the Ram, 96-98 is a mix of SCI-only/analog (for diagnostics and gauges respectively). In late-1998 the Rams started making the transition to CCD. These are referred to by many as the "98.5 changes". The transition to PCI didn't happen until 2002-2003 transition with the 5.9 Magnum trucks retaining the JTEC w/PCI, while the Hemis got the NGC w/PCI (it wasn't until 2005 that the Ram NGC's started using CANbus). With the Jeeps and Durangos, the years vary and you'll need to dig through some info there as I don't really mess with them enough to know the differences as well.
Your swap would be fairly straightforward but you need to confirm what protocol your vehicle has as any transition-year rig should be double checked. I just worked on an early 98 Ram harness (marked Jan 1998 on the ECM if I recall correctly) that was a mix of 98 and 98.5 changes. I would recommend a Ram ECM as these are the least likely to have SKIM issues (though there are ways around it).
To keep yours emissions legal, you'd have to use a 2000 model year ECM (or newer), which will likely be CCD if it's from a Ram. You could find a 1996-99 gauge cluster (you can pick up mine if you want since I'm going to a 05-06 CANbus cluster with my Hemi) and the harness for it. The easiest way to verify what communication bus protocol the ECM has is to look at the wiring on the C3 connector (you will have a twisted pair for CCD and PCI will be a single wire). Your 2000 fuel system will work fine for those year Magnum motors and you'll be able to make all the emissions equipment work together nicely (just use your factory EVAP purge).
What trans are you thinking of using? The AX is a good option if keeping it a manual trans; all you would need is a Dakota 3.9L bellhousing. For an auto trans, the factory 46RE is a good option and works really well with some very minor tweaks/improvements to help with flow. Note that on the auto transmission, the "Dodge" versions all have the starter on the driver-side. For the "Jeep" versions, the starter is on the passenger side. There is only a single year for the Jeep-46RE and those came out of a 1998 5.9L Grand Cherokee (aka. the "niners"). The cores are hard to find but available. These will allow you to use Grand Cherokee headers and have slightly more room underneath. If you use a Dodge-46RE, I recommend you use a 1" BL and Ram shorty-headers due to clearance of the firewall (fits fine otherwise).