Your cranking dwell is pretty low, I'd set it to 6 and see if it works. That's what I use. It may be too low to fire the coils without the alternator charging and if battery voltage is low. On that note, are you using a battery or a charger? Chargers cause electronics to behave erratically. Mine will not behave correctly if I hook the charger up to the car with no battery. The battery actually buffers out noise, even if it is weak.
My running dwell is 3.1, and duration is .7.
The brown signal grounds should be tied into the sensor ground coming out of the MS3. Some people wire them to the power ground location and it works, but it is not recommended nor is it how they were designed to be wired.
The black grounds should definitely be grounded to a solid ground location, ideally AWAY from the MS3 grounds to minimize noise issues. I have my O2 sensor heater grounds and coil grounds grounded at the back of one cylinder head, and the MS3 grounds and O2 sensor grounds to the other head.
If you are certain the coils are wired ok and the setting changes did nothing, connect a headlight bulb across one of the coil connectors 12v and black "power" ground wires. Key on, Engine Off, if the bulb doesn't light up bright you have a weak connection somewhere.
This is a basic load test and will reveal issues a basic volt or ohm meter will not since one strand of a wire could be left intact and you'd pass an ohm check. A load test stress tests the circuit with real life current draw.
If that passes, I'd then check the signal ground and coil wires from the MS3 by ohm testing each from a coil connector end to the DB37. You can ohm test these since virtually no current passes through them.
If ALL of that passes, it sounds like you have a coil issue after all. Did you initially program your MS3 with the coils connected or the fuse installed? That can burn them up since the coils may be commanded on steady during the flash programming. That's why the prompt screen advises them to be unpowered during flashing.
