They're sorta stand-alone - going from auto to manual, the ECU will get angry if you disconnect the TCU. I believe you can go manual to auto without it, but it won't be "perfect" as in exactly like an OEM installed automatic tranny setup. As long as it gets the signals from the NSS (get this with the tranny, that way you don't pay for it separately at the junkyard! Just leave it bolted on and they probably won't charge you separately for it), possibly the brake pedal, and the TPS, I'm pretty sure it'll "just work". Could be wrong on this.
Also, a new ECU will only cost you 20-40 dollars at any you-pull-it, just make sure it's from the same year as your MJ, I'm pretty sure a 91 automatic XJ one should work fine. I'd view the driveshafts as more of a dealbreaker personally, they are harder to track down as MJs are not common in junkyards... at least around here.