It's unfortunate that the GPS tracklog in ArcPad only allows for recording by time. A distance filter would make it easier for your purposes. Is the GPS antenna going to have a view of of the sky (at least partial?), or is it going to be inside a backpack 😞 ? For a four hour trip, to get the best data, I would set up a feature class ahead of time for this purpose and turn off the tracklog. My reasoning is because you can log by distance when collecting a polyline feature in ArcPad using the "distance interval" under your GPS Preferences. I would set this to 5-10 meters. That way if the bus is stopped (which I'm sure it will occasionally), you won't be logging data and end up with a vertex editing nightmare on the backend in ArcMap.
Also, will you have GPSCorrect loaded on the unit or will you just be using the NMEA sentences for GPS?