Attempt at test running a Magnum

I really appreciate the time and knowledge you guys have given me.
Once I get the garage straightened out I'll continue with the engine swap. For the time being ill run it on the Dakota's OBD I computer, but I have a couple of options for engine management and I would like your opinions. I know the factory system has vary little tolerance for aftermarket parts, like the cam and intake. I don't plan on building a race engine or using any power adders like a turbo or super charger.
1. I have the engine bay harness, PDC, and OBD II PCM from possibly a '96 Dakota. The reason I say possible 1996 is that I bought an AX15 transmission from the guy who said it came from that year truck. He also had the harness and two PCM's, one has a Mopar update from 2001 if I'm not mistaken. I assumed the harness was from the same truck and forgot to ask him about it.
2. I built an MS3X for a project years ago but sold the car before I messed with installing it. I know it can do 8 cylinder sequential injection among other things. I understand the wiring and hardware aspect of stand alone systems, but not so much the tuning side of it. There are very good build threads on using MS controllers on Magnum engines with the stock flywheel/trigger wheel and cam sync sensor.
My question is what would make the most sense to install?