I agree with your assessment. It took you time for your body to adjust to smoking cigarettes, and it will take some time for it to adjust to vaping. You are essentually inhaling steam or a hot mist and it can take you some time to adapt.
Do a mouth to lung inhale (as opposed to a direct lung inhale), as this will allow the vapor a second to cool in your mouth.
Avoid vaping at too high of power (voltage or wattage) at first, avoid using too low of coil resistance in your atomizers. Higher pg levels in your Pg/Vg ratio in your e-liquid can cause harshness, as well as too high of a nicotine concentration.
And some flavors just taste harsher to some individuals.