do a 1 mile TT running, 5k TT cycling after a deep warm up (on different days) and those are good starting VO2 paces for you. Then start repeats say 3-7 (depends on ability to maintain intensity) x 2-3 mins or so at the pace you determined in the tests. Eventually you can get up to 3-5 x 8 minute efforts, which is pretty hard. Experienced athletes can get up to 2 miles or 8k cycling distance at that effort for VO2 tests. However, time would be better spent to generally ride more and put in the miles, and don't fear the inclines (unless you plan on sticking to sprint/olympic stuff). Climb a lot. Climb fast, climb slow, climb steady. Embrace the hills and your cycling fitness will catch up.

As far as the physiology is concerned, your numbers may be different, but not "wildly" necessarily. In fact, it is unlikely they would ever be the same for any person because of the different muscular recruitments and environmental factors required for each sport. Also, cycling is more "resistive" in nature, especially if you have a slower cadence, so you can feel muscle fatigue in a different way than you would running. Without getting too deep, there are many things that play into your fatigue and performance between the two. I would hazard a guess that you likely need to work on your generally volume for cycling as well as mechanics and skills for both cycling (your apparent limiter) and running (most stressful on the body, so improved technique never hurts).

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Matt Leu, M.S. Kinesiology
San Pedro Fit Works, Los Angeles, CA
Endurance Athlete and Coach
Consistency/time=results