It could be that you are getting too much nicotine as others have said. It can be something of a conundrum, as it's hard to "sort everything out" when you are still dual using. 3 m.g. is low, but for me, sub0hming didn't agree with my system. It just overwhelmed me with too much vape period, although I did start out at too high a nicotine level. Even at a lower level though, especially as I was transitioning, the sheer volume of vapor was overwhelming and I never felt "great.." My respiratory system was pretty much shot when I started vaping, though. I did much better in the beginning strictly MTL and I really don't vape anything lower than 0.5 coils (and not all the time, either).
You could try reducing your nicotine in your sub0hm device, or you could try restricting airflow/wattage a bit to see if it helps. It might be worthwhile getting an inexpensive MTL topper to put on your setup (something like the Nautilus 2, it has 1.8 and 0.7 coils) and perhaps the 0.7 coil might be a good place to start? It's "slightly sub0hm" but the way the tank is built means that primarily, you will be inhaling a MLT "hit" where the vapor pools in your mouth, and you then inhale it. You may need higher e-liquid in that, but because the volume of vapor would be less, you may not get nic sick in any case. That would be the most inexpensive (but still decent, and a good tank) way to try out MTL vaping and see if it suits you better.
With a MTL vape, you can also vape more frequently, and that may help with your cravings and cigarette detox, as it's fairly normal to chain vape while transitioning, as it feels like a "crutch" or something to "help" with those detox symptoms and etc. I'd say try 6--9 m.g. given what you are vaping now, but you may be able to go higher.
Best of luck, switching can be difficult and frustrating, and many folks don't land on the "right" device initially, but overall the savings are cost effective once you find the right device for you. So, don't give up, and some dual use is pretty normal in the beginning.
Anna