I have almost identical symptoms with my engine. I am also running and MSD 6AL and MSD Pro Billet distributor.
At lower revs, it feels fine, but when cruising at around 3,000rpm, it sounds like it is misfiring and will hesitate and pop if asked to accelerate. Once accelerating, it feels fine again until it settles to an even cruise rpm.
Having read this thread, it sounds like I have to ruin a cap by drilling a large hole in it just to check if the phasing is the problem.
Oh well, needs must I suppose.
One more point, the central terminal in the cap is recessed below the level of the steel ring around it. That doesn't seem right to me, but can someone please confirm. Everything is just over 1 year old and has done less than 3,000 miles.
Paul