tara,
you have it down pretty well, as far as understanding transcription/translation.
one thing from the outset: we do not express all forms of all the genes we have, and there is post-transcriptional AND post-translational changes that cells make that are NOT dictated solely by our genes, but by the conditions present in that cell.
to put it simply, since you clearly get this when i don't blabber science-speak:
muscles have optimal contraction speeds, both for generating power, and for using less energy to generate power. as you work muscles at speeds of contraction outside of optimum, that serves as the stimulus to adapt.
adaptation occurs by "changing out" part of your myosin (the thick filament of a muscle fiber). your muscle can basically mix-and-match different myosin heads as your principle training speeds/racing speeds change (this is why running slow ALL the time makes you slower, incidentally, at least in part). what it seeks to do, if you train at many paces as most of us do (including same pace uphill, that counts as different pace as far as muscles are concerned), is create a RANGE of speeds at which it, the muscle, is comfortable.
we all have, as far as i know, most of the different myosin head genes. the change comes from training "turning on" different ones.
to answer succintly: we have many more genes than we ever use. we have different forms of many proteins. multitudes of stimuli in your lifetime, not just from running, will affect which are used, and in what proportion.
feel free to ask, and i'll do my best to answer. i, like you, am just learning this stuff, and there is a TON i don't know.
cheers,
greg