After all of this discussion I think that I finally understand the idea. In my thought experiment I had a single photon traveling between the mirrors of my light clock. It would seem that instead it is an omnidirectional light source shining through a pinhole. As the light is diffracted it travels along both the x and y axis. If this is correct please let me know so I can put this to rest.
The only other question I have is: Is this light clock actually measuring time? When we set it up we had 2 constants and 1 variable. We couldn't the change speed of light and we knew what we wanted to call one second. Because it is easier for me to think about, I am going to say that every time the light makes one trip up and back down it is one second. So we manipulated the distance between the mirrors (of our now enormously large clock) to be 150,000,000 m Is this clock actually measuring time or is it measuring distance? If it takes longer than 1s to complete the trip the observer would know that the light traveled further than 3 x 10^8 m... Or, the observer could just not care that it traveled further and say hey, the clock ticked, it must be a second that passed. Just because the astronaut is moving with the light and cant see that it is traveling further doesn't mean that time changes, does it? I guess what I am getting at is, if a clock reads that 10 seconds have passed, but thousands of other clocks say 11 seconds have passed wouldn't it make more sense to say that the first clock is broken rather than the first clock traveled to a place where time changes? (seems more parsimonious to me) Why is it that just because the clock says x time has passed we believe it? Further, if time dilation actually works, why are biological clocks affected?
Sorry this was so long, I'm really curious about it. I actually spend the better part of my days trying to make this make sense. All of your answers are GREATLY appreciated.