Are there any exercises to help strengthen the muscles not being used by bicycling to prevent injuries from the over-strengthening of the muscles gained by cycling which could off-set the weaker non-used muscles?

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A regular stretching program is the best thing u can do. Even if u have some muscle groups that r underused, stretching will help to keep them from getting pulled or strained. Weightlifting or cross training in other activities that will use those muscles is the other answer, of course.

It is good to take notice of that part of ur fitness because when u overdo things with one muscle group u really can have some problems in other areas. For instance, serious cyclists r known for overdeveloped hams & quads. This can lead to knee, achilles tendon, & even back problems if it gets too far out of whack.