PCM options
I've got an MS3X running my 5.7 in my 67 Dart currently.
For the long story, I originally swapped the engine into the car with a carb and an MSD box because I was in college and didn't have the money to buy a nice fuel tank with a built in pump (this was 10+ years ago). I also bought the engine with zero electronics other than the sensors that were still mounted, so no harness or PCM to start with. Sold the factory intake to a guy and was just chatting about possibly going back to EFI some day with him when he picked it up and he mentioned he knew someone taking an MS setup off a 340. Called the guy and worked out a screaming deal for a "fuel inject a small block Mopar in a box" kit. Ended up with a 4bbl throttle body, intake, fuel rails, injectors, pump, O2 sensor and controller, MS2, wiring, relay box, etc. Sold off all the stuff I didn't need for the Hemi and think it cost me $200 in the long run for a full MS2 setup. I kept the MSD and ran the MS as a fuel only setup for several years until I decided I wanted to have all the tuning in one place and better control of the ignition. Got the parts for Christmas to upgrade to an MS3X and have really enjoyed the extra functionality it gave me.
Short version of the story is I love tinkering and the open source nature of the Megasquirt line. Pretty much everything I did on the car I did in steps as I learned how it all worked. Began with a fuel only EFI system running off the tach signal from the MSD to a near OEM style setup with table switching, sequential injection, wideband O2 feedback, closed loop idle control, traction control, A/C control (once I actually put A/C in the car), alternator control, several extra gauges for datalogging, etc. Pretty much if I want to do something with the car, there is a way to do it with the MS if I want to.
I was eyeing the Megasquirt system from the start and just happened to find a great deal on one, but I also had a lot less options back when I did the swap. The other option I was looking at back then was a FAST system. They were better known for their TBI kits, but they actually sold a kit that would connect to a factory manifold and 8 injectors instead of their throttle body setup. I almost never saw anyone use or even mention that kit, but it seemed like a nice setup. I think the Holley kits have largely taken over that market though, and are incredibly feature rich nowadays from what I can tell. I think you pay a premium for that though. With the MS I could add features as I went and spread the cost a little more than one big initial hit. I'm guessing a factory PCM would probably give you some of the nicest driveability, but at the cost of having limited modification potential. I know you can tune them, but they are ultimately still a pretty fixed system. I can run an MS as a MAF setup, speed density, alpha-n, etc. at the flip of a setting, so it would adapt to pretty much any mod you'd ever want to do with the car. You don't have to play games and trick the computer into thinking it's doing one thing when you want it to do another (like adding boost to a computer that isn't built for it). The MS lineup has gotten way more professional in the later years as well with nice enclosures and real sealed connectors, but I think they are also going up in price to match, so maybe not as much of a deal as they used to be. I guess that all depends on how much you're willing to tinker though. I've debated more than once about ripping my setup out and moving to one of the modern enclosed units that could mount in the engine bay to clean up my wiring, but I don't think the cost justifies it for me yet.