I've been working shifts on and off for more than 15 years, some of them start at 7 am, some end at 1 am. I've been a cyclist, not a runner but when I tried to put cycling and running together I never ran more than two times/week.
You ARE draining yourself, no wonder you feel under the weather, riding 100 miles and running 4 times/week with intervals.
I am not you, but If I were, I'd run two times a week tops and do only one of them fast.
there were studies of smokers on how much smoking affects VO2max. IIRC smoking takes 2-7% off VO2max, depending on years of smoking accumulated and how much cigs a day. Since I am a bad runner I'd rather not share my VO2max with smoking. Smells bad too...