Not all current Bosch Blue coils are created equal. Cheap Brazilian ones from classic VW Beetle suppliers have a poor reputation. Any 3 ohm internal resistor coil should be fine. Points setting is spec'd at 16-20thou. Don't know what you use but try 16 thou to get a bit more dwell. This will help keep the coil saturated at higher revs, which might help with your misfires.
Basic tuning should start with setting the valve clearances, then the timing and then the carb settings. You've made an adjustment to the carbs but they may still be a bit weak. Baseline 12 flats down (1 1/2 turns). Might be up to 2 flats less or 1 flat more and probably won't be the same for each carb to get the smoothest tick-over.