Yes. The 650's are the same as the 750's as far as plug wires.
Left coil (1&4)
Right coil (2&3)
Make sure the plug wires are solidly seated into the coils, and plug boots. They are held in place on a threaded barb inside the coils, and boots. Over time heat, and vibration can cause these to loosen. If they have loosened to the point of not being secure. You can trim approx 1/4" off the ends of the wires to allow the barbs to get a fresh bite into the wires. If the wires have already been shorten to much to allow any further length to be removed. You can replace the wires with 7-8mm solid core plug wire. Do not use standard automotive carbon thread core plug wires!
Also check to make sure that the plug boots have the correct resistance. There are small resistor elements built into the plug boots. Over time it is possible for these elements to go bad. Plug boot replacement is required if any bad ones are found. I am not sure of the correct resistance for the boots, but they should be 5k, or 10k ohms.
Faulty spark plugs when new are not unheard of. It has happened more than you would think. Swap the non sparking plug with one that does to see if the problem is in the plug.
Other items to check:
Valve clearances
Cam chain tension
Pulse Pick-up clearance
Timing
The 650 has essentially two identical ignition systems that fire 2 cylinders each. Each system contains the pulse pick-up, ignitor, coil, wires, and plugs. These parts are the same for each system despite the differences in color coding of the wiring. You can swap these parts to test, and troubleshoot ignition problems. Most of the time it will be a simple matter of switch the wiring plug ends. The pulse pick-ups will have to be moved in location as well. Otherwise the timing will be 180* off.
Bad ignitors seem to be a side effect of problems with the charging system on the 650's. When the charging systems fails. It appears to cause the ignitors to get hot, and melt the black potting material out of the ignitors. This does not make the ignitor bad unless the charging system goes unrepaired. Eventually the ignitors will get hot enough to burn themselves out. The potting material can be replace with JBWeld.
When you rebuilt the carbs. Did you remove the pilot/slow jets, and clean them also?
Despite the common incorrect knowledge. The pressed in pilot/slow jets can be removed for cleaning/replacing. Once clean they can be pressed back in.