Considering a 5.9 EFI swap into 68 Val -833 O/D car
Megasquirt is a "stand alone" system so you wouldn't need the factory PCM. Just really the engine harness for some connectors. Obviously you have to connect all the wires from their harness yourself so that's a bit time consuming. The ones from DIYAutoTune have their own markings for what they go to so it's not that terrible.
I've talked to a lot of people that have Megasquirt systems and so long as they did a decent job tuning and they either bought a pro-assembled one or did a good job soldering their DIY kit together, I really haven't seen any problems.
There is a bit of a learning curve but now they've gotten to the point that you basically program your parameters and you can use VE Analyze live to get the tune worked in pretty good in the driveability section automatically. There are also people that can look at your file online and the logs and help you make changes.