Definitely allergies. You need to be taking flonase everyday for something like a week or two before it's at full strength in your system. Also, take a benadryl after to calm the irritation. Stuff like claratin/flonase are to prevent allergies. They can't help much to reduce the symptoms once they're happening, you need benadryl for that.

I have that when the air is cold, doc said its asthma. Have an inhaler now.

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asthma, exacerbated by allergies and/or exercise..

Sean H advice is good.

I've had exercise-induced for a decade or so, never had an allergy problem but ended up in ER last week unable to breathe, without even getting any exercise in :-(
Doc said they have seen an unusual number of extreme asthma cases this year, may be a bad pollen year or some effect of the fires and smoke over the West US..

I use a medication called Montelukast 10mg. Taken daily during the allergy season. Ask your doctor...

yes often when high moisture and cold or Late Aug through Oct when allergies are bad here for me. Somedays can be very bad.

Nasonex, allegra, and singular.

This might be separate events. It is fairly typical, especially in higher-level athletes to have some sort of exercise induced asthma. The longer and/or harder the session the greater the likelihood this happens and the coughing presents itself after the exercise and not during. Go to an Olympic triathlon and watch the athletes at the pointy end after the race and many will be coughing uncontrollably . Usually if you bring your effort down slowly you can avoid this, but in a race that isn't really possible. I had this most recently post Ironman Wisconsin, hacked up a lung afterward.

Having it during the exercise, like your run, sounds a bit different and is very likely a result of those season allergies you suggest.

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Feeling it on the run was residual from the day before....I definitely feel it most, after a long ride...but I can feel it starting to happen near the end of those long rides.

Ummm. . .Benadryl is a first generation antihistamine. Claritin is a 2nd generation antihistamine with less sedating side effects. Either is effective with allergies. I agree that Flonase does take a week or two to kick in

I am not so sure as to whether it is asthma vs allergies vs some other. If it was asthma I'd expect it to happen sooner rather than at the end of a 5-7 hour ride. Do you have drainage, congestion? Did the premedication with the meds help?