Something my doctor told me on one of my previous "quits"... I have asthma and had noticed a month or so, maybe 6 weeks, after I quit smoking, my asthma was a LOT worse than it had been when I was smoking (this was several years ago, WAY before ever vaping). She told me that because of all the tar and crap that are in the tobacco cigs, the cilia in the lungs were all gunked up and basically kinda lying down while I was smoking. Once I stopped, they started working their way free again... And in that process, all the tar and gunk was breaking loose, making my breathing condition temporarily worse. I'm not a doctor, of course, so I can't say this is the same thing you're experiencing, just saying that it's a possibility. And it DOES get better, but it takes time, of course. And, obviously, having just recovered from pneumonia may play into it as well.
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A couple of my friends told me more or less the same thing. I did start coughing up some very, very thick phlegm about two weeks ago.
I'm determined to stick with the vaping, though - I just ordered a bottle of 100%pg and an 80/20 mix (I didn't see an option for 100%vg) of the same flavor from Vapor Bomb, as swedishfish suggested.