My first thought is you need a new engine tuner. These engines are pretty simple. A carb rebuild or purchase a new one would solve most of that problem. The ignition sounds like a big part of your problem. Sticky weights, springs, bushings, faulty vacuum advance and then throw a MSD ignition at it and you create a lot more opportunity for problems. A simple HEI upgrade can solve most problems with the lower rpm's that most of these engines run at.
Like you mentioned keep the original parts incase you want them again.
Moving on with a newer engine has it's pros and cons. If your keeping the car do what you want with the car.
I for one would be interested in your updates and how you make it all work.
Good Luck