I'm back. I have been working out sporadically, but I just finished my third round of antibiotics for this lingering cough and it's still not gone. I went to my longtime allergist/immunologist due to being unable to kick this and she is now of the opinion that there is something larger going on. She's launching a full workup on me that will help determine if I have bronchiectasis, atypical CF, or GERD-related chronic bronchitis. I should have a better idea by the end of the month.
I've been back to boot camp for over a week now and I am back to running as well. My doctor said it is ok for me to resume running because it's obviously a chronic issue and it's better for me to run and cough up what I can. Also... We've gotten a home gym, so I'm doing core work at least 4 times a week. I managed to only gain 1.5 lbs over the holidays and got that off in less than a week and am now at a new low.

Anyway... tonight. 4.86 miles in 57 minutes. In 27 degrees with 17 degree wind chill and falling snow!!! I'm starting to feel a bit more like a hard core runner.
I also did a 5k Resolution Run on New Years' Eve in 22 degrees and didn't PR, but managed to be within 35 seconds of my PR, even being sick! I'm proud of myself for pushing through.