DistanceFromCall means the distance that the bus is from the stop, linearly referenced along the route, in meters.
CallDistanceAlongRoute means the distance the stop is from the beginning of the route, linearly referenced, in meters.
As to what happens when we don't get GPS data for a brief period from a particular bus -- we continue to report its location at the last location it sent in. The timestamp of the last observation is part of the SIRI API (RecordedAtTime I think). In the customer-facing UI's, we:
1. report the data as "old" if we haven't gotten an update in more than some configurable threshlod (2 minutes I believe)
2. stop showing the bus if we haven't gotten an update in more than some configurable threshlod (5 minutes I believe)
As for your question about Routes, how they are sorted, etc. I don't really understand what you are asking. Some more specifics would be good. For example, the URL of the particular page you are looking at or API call you are using.
Thanks,
Mike