Hi everyone, thanks for all of the info. Sorry getting back to reply so late, but I got called away for work.
I found the problem. A month ago, I had a motorcycle shop do a full clean of the carbs and replace some of the internal wear bits. Since I had done the ear shave and have the Vance & Hines exhaust, I have the larger pilot/main jets. Well, when they put it back together, they used the stock size jets. I could visually tell the main jets were too small.
I got new, proper size jets and put them in this morning, and it does sound better. I'm guessing the bike was running lean, causing the engine to run hotter. With the lean condition and hot engine while idling for a while at a light, the engine would stall when I tried to give it a little throttle.
I'll test it out with a full run through traffic, but I'm pretty sure it will run better and cooler and not stall out.
Also, I will try to do those two mods, one for the gap in the timing sensors and the other with the relay for the coil at a later time.
I'm not a newbie, but haven't been around the forums in a while due to work and wrenching on a couple of our classic cars. Now that they are done, I'm getting back working on my bike and transforming it to flat black with some red accents. I'll post my bits in the "hello" section of the forum.