It could be plausible. As many people have commented, varying the type/intensity of training and diet alone will not make up the difference. But who knows what could happen with a wholistic lifestyle change that is radically different (but perhaps superior to) that of other athletes.
Maybe the Neural Network realizes the ideal training cycle for his body is 15 hours per cycle. Not many people live on anything other than a 24 hour cycle, and while it's true that life has generally adapted towards this, it may not be the optimum for transforming into a perfect Olympian.
Or, for easier math, maybe he does 12 hour cycles of 30 min eat -> 2 hours workout -> 30 min eat -> 2 hours workout -> 30 min eat -> 2 hours workout -> 4.5 hours sleep. In 24 hours he'll work out 12 hours, eat 6 times, and sleep 9 hours.
The demands placed on the mind and body by this training regimen, long term, would be extremely high. The Neural Network would need to be able to motivate him highly, or induce a long term trancelike state where he is highly susceptible to suggestion and follows orders when any sane human would quit from exhaustion.
Also he'd likely need access to training equipment beyond just running. Run too much and your body breaks down. Combination of low-impact water-resistance activities (water cycling, water running, swimming) and direct electrical stimulation of muscles in Neural Network determined patterns.
He'd accomplish no work outside of his training, no time for socializing of any form, and the cumulative stress might push his body to the breaking point right after the marathon (collapse with a heart attack crossing the finish line). 790
Maybe the Neural Network knew this but didn't tell him because it would impact his motivation for training.
Even then, maybe it requires special circumstances for him to win. Like moderate rain during the marathon. Most competitors start out slower, and no one chases the underdog who goes out fast. No one can draft off of him, and he unexpectedly holds on to win with a time 15 minutes slower than the world record marathon, but still faster than what the other competitors did that race. Again, Neural Network might even know that him winning is a long shot, but lie to bolster his confidence, and in your story rainy conditions just so happen to occur.
Even with such an advanced AI, I don't think he could remain at the top of the Marathoning field for say, 4 years (enough to win 2 Olympic gold medals). You generally need to win the genetic lottery in a big way to get near the top, as others have stated. You might fudge your way in with absolute perfect preparation as an average joe, for one performance under ideal circumstances, but sooner or later your "averageness" is going to catch up with you. Most human bodies cannot handle the stress of performing at an elite level over a sustained period of time.
Of course, this AI has already gone far beyond just proper diet/training, but I'd be willing to believe this one, if the author met me half way and acknowledged that in the end, even with all this (near-suicidal) prep, it was a 50/50 gamble. 790