I am changing distributors and coils today but wanted to know what everyone thought.

When engine was brand new the only thing unchanged was the distributor, MSD6a, and Mallory coil. The truck ran like a champ and had incredible power from idle to redline. Now all of a sudden it sputters from idle to 1500rpm and doesnt rev freely to 5500, redline from engine builder is 6500. Engine when new ran high 12s in the 1/4...now runs high 13s with 4000 miles. I have changed timing many times with no change in power. The timing light does sputter over 2500 rpm at close to the same duration of flash at idle. Some people tell me the MSD box is burnt up because it sat for 2 years before being used again. Others say the distributor is the problem or the coil. I have changed everything else on the engine except these things but today I am putting on a Mallory HEI unit and not using the MSD box. I wanted everyones opinion on possible fixes or support that this will solve my problem. Thanks for your time and patience.