I swapped a BA turbo engine into my BA wagon. Both cars were auto which made it easier. I wanted to keep it easy for me in that I didnt want to take the car somewhere to get the PCM flashed to get it going. Its not exactly what you are doing but its just an example and might prompt you to think about some of the other issues you will come across.
I had to install a turbo engine bay loom (or N/A XR6 as previously mentioned) which has the plug for wastgate solenoid. This required removing the drivers side guard. The passenger side loom was just the additional third plug plus loom on the PCM for wastegate. I swapped in the PCM and BEM from the donor car. I also had to swap the dash loom as it has extra wiring for T/C light in the cluster, wiring for the auto headlight sensor and a few other things. This meant the whole dash came out. The wagon was only a 3 channel ABS sensor car so I had to swap the ABS module for the 4 channel one out of the turbo car. This also required a second brake line running from the front to back of the car. The rear brakes are normally on one circuit on the wagon and the turbo ABS module requires two lines. I used the existing airbag/restraint module.
There is a program called Forscan that I used to delete the turbo keys from the PCM and BCM so I could use my wagon keys (wagon steering column). This process was relatively easy but I couldn't find much info on it before I started. Installing the turbo engine, turbo trans and intercooler etc was the easy bit. The only outstanding thing is that the car has a 3.23 ratio diff whereas the donor car had a 3.45. Speedo is not out as the speed is measured from the wheel ABS sensors. The only part I paid someone for was to make the rear section of the exhaust over the diff.
In your case, you have the pedal assembly to swap, clutch reservoir, wastegate solenoid, engine bay loom or just the wiring for the solenoid if you want to save a bit of time, tailshaft... The diff will be fine to get it mobile but as has been said it might not last too long. In saying that, my M78 wagon diff with an LSD has held up fine but its just a stock tune.
Your biggest hurdle will be because you are installing an earlier series engine into a later series car and I expect you will have to take it somewhere to sort the PCM out so it talks with the rest of your car and you can start it UNLESS you change everything so the PATS system is happy. If you are getting it tuned anyway they can probably sort that stuff out for you anyway. Will just need to get towed there.