My question deals with duathlons. I have a solid base of running, about two years of 15 to 25 miles per week and most recently a considerable amount of cycling. In the last two months I have competed in two duathlons and after about 1k into the second run I have been developing a sideache which stops me from running. I have tried slowing down and also breathing deeply from the stomach, neither have helped. This problem only has occurred after a run, bike, run and not during any other runs. The duathlons have been 5k-40k-5k and 5k-20k-5k. Any
Sideaches are related to the diaphragm going into a tetanic spasm. Why this occurs only during your second run in duathelons is open to speculation. Typically a skeletal muscle, like the diaphragm, has to be physiologically fatigued before it can develop a tetanic contraction (which is in fact a function consecutive motor impulses summating, leading to a continuous contraction).
I wonder if your respiration has different qualities (depth, rate, etc) while on the bike. You probably need to train by riding then biking to help best prepare you for the event.
Give that a try.