I had the exact same issue. I had no power for the longest time and kept rebuilding the carbs. Then one day I accidentally brushed the exhaust after running it and found it was cool enough to touch. I figured that it wasn't sparking on that cylinder. I took the plug out and turned it over a couple of times--saw spark and put it back in. I still couldn't get that cylinder to fire. I thought it might be compression. Ran a compression test and leak down test--everything was within spec.
Finally I bought a Dynatek all-in-one Signal Generator/Ignitor combo. I installed it on my 1980 GS450 using the stock mechanical advance, but replacing the stock magnetic rotor with theirs. I also had to machine a washer to use as a spacer over the end of the rotor. The new rotor was a bit shorter than the stock. You have to use non-magnetic material for the spacer. The kit came with new coils, but not the spark plug wires. The stock coils have the wires integrated into them and you can replace the boots. I had to pick up some wires and cut them down to fit. You need 8mm wires.
...Long story short. My GS450 Runs like a Beast!!!
I have also since rebuilt the carbs. I have a great source for a carb kit(s) (all new orings/needle and seat/K&N Pods/Main Jet/Pilot Jet/Air Jet/Dust Caps/intake boots/gaskets/hex bolt kit). Includes everything but the diaphrams, which I can get but those are pretty pricey. As you know they don't build kits for those Mikuni BSS34 CV carbs because of the EPA regulations. I pretty much assembled this kit through various sources. I will also rebuild carbs.
I also recently rebuilt the brake caliper, replaced and repacked all the bearings, built a fiberglass seat cowl, replaced the tires, and removed the old handlebars for clip-ons.
Lastly, I will say that I too changed out for the ElectroSport Stator and Regulator/Rectifier. The charging system runs like a champ. i have noticed all the difference from the terribly wimpy OEM system. I am switching up this weekend to a Lithium Iron Phosphate Battery. I moved all my electronics under the seat except the battery so far. I plan to put that new/smaller/lighter battery under the seat as well. A cafe Racer just doesn't look right unless it is clean.
I think I am getting to where I want to be with this project. I plan to do that battery this week and finish that bothersome seat pad. The thing is like riding a park bench. lol