The MTB is not the best solution but I ride one with front suspension locked out so it basically a heavy hard fork. I took the knobbies off asap as well and put some street tires on. That helped a lot.

Those are the two biggest issues you'll see with the MTB. The weight and the wind will be an issue forever but eventually you'll get the strength to push past it for the most part.

Burning out is a big concern really. Start slow and let the legs rest. If you can't get a ride any other way then ride the bike but take it super easy. Like just fast enough to not fall off easy. Keep the bike geared down so you are not "mashing" the pedals and that'll help with the fatigue and the cardio. Hills always suck but you learn how to deal with them and as the stamina in the legs build up they become less of an issue but they always sucks. lol

I have been riding my 16 mile round trip commute 3-5 days a week since about March. I still feel the burn and I still get tired but not to the point of exhaustion like you are talking about. As it should be I would hope. I find my self pushing harder and harder as the time goes by. I am averaging 14-15 mph at this point and I have added loads to my MTB since I got it as far as weight is concerned but I have also lost 20 lbs.

That amount of time off the bike will certainly set you back a bit. I would look at the Flonase option as mentioned before and see if that helps.