Feeling awful after intense workouts

It sounds like you've already checked out a number of medical possibilities so not sure I can be any help but, having suffered through a lot of hard run workouts in my life, I can think of a few things:

*Cooldown and recovery. What happens after you finish the intervals or tempo? Are you doing an adequate cooldown at a very easy pace? I trained with a very high-powered team in college, and I know that for some of them, their "cooldown" pace was simply not an easy run for me. Maybe you are getting an inadequate cooldown either due to time pressure to get back to work (or home or wherever) or keeping up with faster runners to be social? People differ in how much they need but if you are doing less than 10-15 minutes, you might try a longer, easier cooldown.

*Timing of refueling/rehydration after the workouts. If you wait too long, it can delay recovery.

*Sleep/recovery. Not getting enough in general, and/or poor sleep quality after an intense workout. I can't tell from your post if you are doing these workouts mainly early AM or in the evening. If the latter, cooldown (both from the workout and in a more general sense) becomes more important. Back when I did most of my training after work, I struggled with insomnia and some other issues (migraines after workouts, asthma at night). There was no physical cause and one doctor who did endurance sports suggested it might be more of a nervous system arousal issue. Hard training is both physically and mentally stimulating and gets the body into "go" mode with elevated core temp, heart rate, breathing, all sorts of stress hormones, lactic acid. If you try to move quickly to "rest" mode without adequate cooldown, cooling, and mentally relaxing "down time" (which not everyone has time for in late evening), it can seriously affect sleep and feelings of well-being. In my case, this was compounded by training in tropical heat and at a time of day when air quality was worse. I finally moved all my bike and run workouts to early AM, and rarely have such issues anymore.

*Effort level. Maybe you are simply hitting the paces a bit too hard for your current fitness. That is easy to do in a timed, group workout situation. Have you determined the paces based on race results or an LT test? Even if you have, you may have to modify the "theoretical" paces from the charts a little until your body is used to a higher level of intensity. With most of those pace charts, an athlete will perform somewhat better/more comfortably at the distance they have more experience and/or natural aptitude for. It's rare for pace charts to truly show equivalent efforts for an individual.

You mention that you are coming from an IM training background with mainly aerobic efforts, Track intervals and tempo runs are different animals. My run background was mainly in 5 and 10K at high school and college level, so I've done my share of intense running. In recent years, I've mainly focused on tri, especially HIM. Pretty much every time I do a sprint tri, I feel ill (in the manner you've described) through most of the run and up to 24 hours after the race. It's just a higher level of intensity than HIM training typically prepares me for. I have the speed to be competitive in my AG in a sprint, but it often seems harder to gut out a sprint tri than do a good HIM. I'm quite sure if I tried to do one of my high school or college track workouts at the same level of intensity (adjusted for age and fitness), I'd feel the same way. Maybe try backing off the paces a bit, or running with the HR monitor again and backing off if your HR gets above a certain level, rather than just trying to hang with a group?

*Finally, if these workouts are early AM, caffeine? Most of my intense biking/running is done between 5 and 6:30 in the morning, and then I go to teach fifth grade and coach for 8-10 hours after. Not sure I could cope without a couple of espresso shots before the kiddos arrive!

Thank you for such an informative post.