Spent a good amount of time perusing the wiring diagrams in the 98 and 94 FSMs.
What I found out:
* the 94 ECU doesn't appear to have a CCD bus interface, at least not in the manner I am used to. It's OBD-I of course, and has the old style diagnostic port under the hood, and I can't find any reference to a CCD bus in its pinout. It has separate leads going to the instrument cluster for tach, VSS, oil pressure, temp, fuel level, etc, just as a 96 and earlier XJ ECU+IP does. So a 94 ECU (and probably others, Bloose said the 98 is the year you want, I'll trust him on that and assume 95-97 are also not CCD) would work nicely if you were swapping this drivetrain in and combining it with a 96 and earlier XJ/MJ interior, but that's not what I'm aiming for.
* the 98 ECU does appear to have a CCD bus interface, just like Bloose said. Fancy that!
So I'm going to investigate whether I can get my 98 5.2 Auto ECU reprogrammed to be a 98 5.9 Manual ECU. If I can, great, if I can't, off to eBay I go!
Side note: I am so used to there being a separate ECU and TCU that I tend to use those names. 2.5L XJs/MJs and (it seems) most Dodge vehicles have a single combined module that controls both, so PCM would be a more accurate term. If you see me say ECU in this thread, I mean PCM.
I'm going to use as many of the sensors and senders off the 94 powertrain as I can just to simplify wiring harness modification. My bet is that almost everything is the same with different connector shapes, similar to how XJ senders are mostly the same but change connector shapes around 95/96/97/98, but I'll have to verify this (for instance I know 91 through 01 XJ CPSes are all the same electrically, but have 3 different connectors over the years for some stupid reason.) In any case it will involve a lot of looking up part applications / year splits, so I'll probably end up knowing more about Dodge powertrain senders than I ever wanted to.