Challenga

I have an 88 with a 3.0 V6 with a miss that I can't figure out. I bought the 4runner out of a someones backyard an it didn't run. I have replaced the head gaskets and did a little work on the heads. I replaced the valve seals and lapped the valves by hand. I have put the thing back together and it started right up. Runs like a top, but it has a miss and a lack of power. It takes off great from a stop, but it has a hard time with hills and going above 45. This weekend I got up and decided to get to the bottom of the miss.

I pulled the spark plugs and found that number six looked a little black and smelled like fuel. I decided I would check to make sure the spark plug was getting fire. Keep in mind that the spark plugs, wires, and distributer are new. I put an old spark plug on the wire and grounded it while starting. It has spark. It seemed a little irregular, but it had spark. So I hooked up the timing light to the wires while it was running just as a secondary check for fire. When I tapped onto the wires on the left, the light blinked like normal. When I hooked on the wires on the right, the light was either on constant or the light was blinking so fast that it looked constant. And it was blinking a little bit irregular. It had a couple of brighter blinks and a couple of blinks.

Does anyone know where I should start. I am a V8 guy and know motors pretty well, but this does not make sense to me. The distributor turns at a constant speed, how does would the light blink differently on the left wires than the right wires?

I will be working on this all day today (or until I figure it out), so if you have any ideas let me know?

Ben