First, congratulations on quitting!
You are correct that smoking tends to lower estrogen levels. One theory is that it increases the rate at which the liver metabolizes estrogen, leaving less estrogen in the bloodstream:
It could very well be that the increase in estrogen level after you quit smoking may have exacerbated the endo that you had, causing you to start to have symptoms. However, you have done so much good for your health in so many ways, one of which is that your risk of osteoporosis is going to be much lower.
Also, it appears that Alzheimer's is much more common in smokers on HRT than in nonsmokers on HRT:
And it seems that among all women who develop breast cancer postmenopausally, smokers tend to develop estrogen-negative breast cancers much more than nonsmokers do. This is an important difference because estrogen-positive cancers tend to be easier to treat and have a better prognosis.
Finally, smokers on HRT have a much higher risk of MI (myocardial infarction) than women on HRT who do not smoke.
So, enjoy the fresh air knowing you have done a good thing for yourself.