So the PiKelet project is almost at an end. I have achieved what I was aiming for, wiuth a few minor edits. It now boots into the pixel desktop without any issue. The USB hub works fine to power a keyboard and mouse. At this point it can be used as a complete Raspberry Pi Computer running Raspbian.

It is a useful, rugged piece of hardware that is flexible enough to be used for several purposes. I am not sure what the final use for the PiKelet will be. But it is WiFi connected and can be connected via the uart. I will add some code to make the status indicator LED more useful. I hope this build log will help someone in a future project.