You did the right thing sending that MSD distributor back. I'll take a guess and say it's model # 8366? Google MSD 8366 problems and see what I mean. Some people have had OK luck with them by running a real GM module, but the fact is those distributors are bad news. You'd think you could get a good product by going with a "trusted" name, but that 8366 is junk.
If you suspected your original distributor, and now it's reinstalled and still having problems - I'd replace it with another OEM distributor, especially if the magnets seem very weak. They're not very strong to begin with, so it may be hard to tell for sure if they're bad unless they have no real magnetism at all (or are broken.)
A distinct possibility is the coil may be bad, but I can't really tell you what the probability of it would be.
I'm not a fan of most parts-house brand ignition parts; even the "big names" like Borg Warner. Even the top-line NAPA stuff is often chinese-made anymore, though it doesn't hurt to go down there and check it out for yourself. Their cheap-line stuff isn't worth buying, might as well gamble with Vatozone or Pest Boys at that point.
On the subject of the heat sink compound / "thermal grease" - more is less in this case; some people goop it on - not saying you did - but a thin layer is what is best. Too much acts more like an insulator than helping with heat transfer. It's best to clean the surfaces well and apply a new thin layer of the stuff when installing a new module.
I'd also check the grounds around the engine. Most important would be the rear passenger head ground strap to the body; goes to the firewall just under the heater hoses. It gets corroded kind of easily, or gets broken / left off if the engine has ever been out and the installer missed the strap.