When you say "If we ride to Pittsburgh we arrive at 4:45am, which if we put our bikes together"
I assume you mean the train arrives in Pittsburgh at 4:45? That sounds about right as far as times.
I would start from the Pittsburgh end from the sound of train arrival. By the time you get the bikes put together, there plenty of daylight.
I would not have any issues with putting the bikes together in the station but I am not sure. If you chose arrive by train in Pittsburgh option then I will scout out the station this week and see if there are out of the way places to work. My guess there is, Pittsburgh is not a huge destination for trains.
What is your intended arrival day? Assuming I have the day off I could meet you in town and give you a little tour of the Burgh, including Bicycle Heaven. You can't miss that. Then I could guide you the "safe" way to the new trail to the GAP.