What you are asking for is too much, too soon. If you lost a whole year of running due to an injury, you should expect to take at least that long to regain lost fitness. In other words, running full workouts during your recovery time was banking on fitness you no longer had, resulting in further injury, and another increase in recovery time.
I agree with Jim that the Peroneal assertion, as stated, is suspect, but perhaps a misunderstanding on your part of what the chiropractor actually said. Peroneals (aka fibularis muscles) are, for the most part, pronating muscles, used to evert the foot. An overused Peroneal muscle could be tight or weak, but if tight, could force the Tibialis Posterior muscle to tire and collapse the arch, as Jim indicated, and the chiropractor probably meant to say. Tib P works in opposition to the Peroneals, and tends to relax from stress rather than tighten, leading to less support for the arch, stretching of the plantar fascia, alteration of the gait, and likely chronic pain for a runner. This is probably what JJR was referring to by "major player."
I'm not sure what rehab was done for this injury, but you should not be running on a collapsed arch. Your coach needs to pay better attention to your physical fitness before allowing you to run, especially before running full workouts. That is not a good strategy for recovery, as you unfortunately found out. You may have pushed to remain on the team, but the primary professional responsibility is to safeguard your health. If you have not experienced a miracle recovery by now, please scrap the aggressive training.
I think JJR is on to something when mentioning the contributions of the hips to compensation injuries, but the hip and core muscles themselves often compensate for structural problems in the leg and foot. My guess is that your feet are built to overpronate, and the shortness of your rise to success in running did not allow time for the rest of your body to adapt to this stress. The peroneals probably tightened, the hip muscles probably began to malfunction, and the Tib P probably released the arch in a cascade of doom for your ambitions as a runner.
I've seen this before, in others as well as myself. Early in my aggressive running history, I developed similar pain, stiffness in the peroneals, and loss of loft to the arch of one foot, as measured by a local running store pro. Full recovery was a long way off, including 6 months of no running at all, and over a year to slowly regain, and eventually exceed, my earlier fitness. Patience was key, but I also began to study this stuff for a living. Measuring the bones in my "bad" foot, it was apparent that the structure forced some unhealthy adaptations, and like you, I paid a price in pain and loss of function. There was also a difference between the length of my legs, the "bad" one being shorter. While this can be an actual physical difference, it can also be due to an imbalance in hip muscle tone.
While muscular problems can be circular in nature, defying our best efforts to find an original cause, bone abnormalities are more permanent. It is likely the bones of your foot are similar to mine, and inherent instability requires more work on the part of your stabilizing muscles, as JJR mentioned regarding the hips. My money is on the foot as the original cause, but the effects get spread out like a game of whack-a-mole. Yes, you can treat your Peroneal muscles, jack up the arch with an orthotic, brace and wrap to improve stability, but the original cause of the problem will continue to precipitate it.
When your foot hits the ground, the load is spread out across the arch when present, normally in order from lateral to medial during the pronation phase. What deepens the pronation phase to a dangerous level, is the need to direct the pressure of impact to the strongest part of the foot. This need increases roughly in inverse proportion to the ability of the rest of the foot to bear impact and/or weight. If during the propulsion phase, force is somehow shifted to weaker structures, the foot will be pronated to return to the strongest position, on the thicker 1st metatarsal of the foot. If the remaining metatarsals are arranged in such a way that pressure is evenly distributed among them, there is less need to deepen or remain in pronation. In my case, the first metarsal bone was too short in relation to the second, and pressure had to be shifted away from the less durable 2nd metatarsal during the propulsion phase, to the first. This action requires more work from the Peroneal muscles, and can tire the Tib P resulting in a relaxation of the arch, and further problems dealing with impact.
Understanding this problem does not involve rocket science, and is logical and accessible to the average runner. It is rarely discussed in the medical approach to injuries, because rhere are so many resulting symptoms to distract from the root cause.
My advice is to have your feet analyzed for their inherent stability, before attempting to subject them to the rigors of cross--country running. While some orthotics can be crafted to compensate for this type of structure, most cusrom orthotics simply mold to the foot as it is, doing nothing to improve upon the basic alignment. Such orthotics perform more as a crutch, and do not restore normal action to the foot via the controlling muscles. Instead, the critical muscles can de-condition from not being used, making the problem worse after time, as Jim mentioned above.