Footflaps - shame you didn't continue to exhaustion on those. I'm not talking about 'top end' as in functional threshold, I'm talking about top-end as in absolute max burst power.
Absolute max means very little in terms of cycling performance.
Are you a track sprinter? Unless it is a very short event, aerobic fitness is always key.
Just going back to your original post as well...
because since running I am not breathing particularly hard at any point when cycling, it's the leg pain that limits me.
Have you tried increasing your running pace or are you consistently running at the same effort over longer distances?
Leg pain in cycling, for me, comes in different forms.
Long threshold intervals @ 100% FTP are uncomfortable by their very nature. As are Vo2 efforts of appx 106%-120%, in much the same way. Its muscle exhaustion that limits how long your can output a set power for. The muscle can only do so much work.
Absolute maximal anaerobic efforts normally leave me unable to physically turn the cranks for a few minutes afterwards. Short 1 mile TT sprints, 1 minute hill climb TT sort of thing.
To me these feel like holding your breath sort of pain, like the muscles are being starved of oxygen, as ultimately they are. But at the end of the day it is still muscle exhaustion, just via a quicker route.