Okay where to start, I just signed up as I've been reading the forums a lot . . .
Welcome, Chaosmoto! Looks like you've pared that bike down to the essentials—good looking. What speedometer are you using? Did you wire it up yourself?
How many miles on the bike? How much was it ridden before you got a hold of it?When you write that you "believe" something is "good", what is the basis for your belief—experience, appearance, professional reference manuals, instrument readings? If the "plugs were "a little black", does that mean sooty or oily? All of them or some of them? You write that you're unsure which direction to head.
This troubleshooting guide created by Bert Vogel contains much helpful information including an explanation of why there was no change in performance when you reversed the #1 and #4 plug wires. If it were my bike, I'd start at the top of the following list and work down it. The bike may start running well after the first few items or you may need to do all of it, and follow through with closer examination of individual components. Explanations are contained in the guide.
What is the battery voltage output?
Has the tank been inspected for sludge?
Has the fuel filter been replaced or it's age determined?
Have all electrical connectors, plug wires, coil connections and fuses, including the four pin connector under the tank, been checked and securely fastened?Have all the rubber components been checked for leaks—the vacuum fitting caps, the throttle body bushings, the air box connections, the fuel pressure regulator vacuum hose?
Have the valves been adjusted and the throttle bodies been balanced?
If none of this has occurred, start at the top of the list and check off each until it is running better, finishing with the valve adjustment/throttle body balance.
Yours is not an unusual circumstance at all. I've read about it repeatedly. The reasons vary.