OK I'm going to be all over the place here, so just be aware. I like Megasquirt for my custom cars, I find that it just lets me do more than some of the out-of-the-box systems. I have run an older version of the Holley TBI and had no problems with it. The new Edelbrock MPI system kinda has me drooling to get a Javelin to try it on. I think that the biggest and most important idea with going to any of these systems is personal knowlege. Know what you need vs. what you want and look for what will get your there the easiest. OTB systems may not offer a wide enough range of parameters for some people, while fully programble units might offer too many. I also support building kit from scratch/junk-yards, I just think it's fun.
1968 M715-Driveway queen/in progress