I occasionally have a situation where I'll be riding along and out of the blue the engine will act like its lost a cylinder or something. It runs like this for a while then snaps out of it and returns to normal. It almost feels like its starving for fuel. It did this once before I replaced the points with dynas. And since the dyna replacement its ran great except yesterday it happened

I've put about 5000 miles on it since I got it last summer and it currently has 55000. Stock everything except dyna "points" which I installed last week. When I finally got them set perfect it started and ran the best its ever ran. Last year it did this once on my ride home and snapped out of it. At that time I checked my battery connections and misc wiring that I had easy access to. The neg terminal on the battery was a little loose so I tightened it up and didn't have the problem again until yesterday.I replaced the plugs(with the dyna "points"), and set the valves, fresh oil, and a splash of mmo in the crankcase and fuel tank. I have Randakks fancy fuel filter that I installed last fall. I rode about 35 miles at highway speed to the barber shop and it was perfect. On my ride home, after about 30 miles of trouble free riding it did this power loss/bogg thing.
This morning it started great and took off like a bat out of hell but "messed up" after about 5 miles.
I've been on vacation and just got back. Before I left I replaced the factory coils with dyna coils and built some new wires. I also put a little seafoam in the gas. It started great this morning and I went for a ride. It ran great for about 3 miles at highway speed+ and, again did the bog/drop cylinder thing. This time it sort of switched back and forth between normal and boggy before it stayed "bad". I came home and sat down at the computer. What should I check next. I am assuming the coils and wires are ok. Is it wrong to make that assumption? With the new electronic "points" and coils the condenser and that ceramic thingy have been eliminated. Plugs wires, "points", and coils are all that's left. What is left to check?