Just a thought... A few years ago I was having a problem similar to yours. It started out looking like a coil was arcing to the bottom of the tank. I bought a set of Accel coils and wires. Seemed to fix the problem. Then it started again. I couldn't see any arcing this time, but it felt the same. It turned out it was one of my brand new plug wires. I did a little research and ended up putting a set of Magnecor race wires on it. Never had the problem again. I've probably got 20,000 miles on it since then. I had to give them the dimensions etc of my wires and they made a set up for me....
http://www.magnecor.com/