SFMTA has historical AVL GPS data for their buses at ftp://avl-data.sfmta.com/avl_data/avl_raw. In each record, there is a train_assignment, which you should be able to link to the route information, however, I am unable to find a match.
from the readme file (ftp://avl-data.sfmta.com/avl_data/avl_raw/read_me.txt)
Linking Data to the SFMTA Schedule: To link the raw AVL data to a schedule you will need to use (1) the GTFS data at --> http://www.sfmta.com/cms/asite/labsindx.htm, (2) file "lookUpSignUpPeriods.csv" and (3) file "lookUpBlockIDToBlockNumNam.csv". File "lookUpBlockIDToBlockNumNam.csv" will allow you to link the block/train numbers in field "TRAIN_ASSIGNMENT" to field "block_id" in file "trips.txt" of the GTFS dataset. File "lookUpSignUpPeriods.csv" gives the dates for which each signup ID is valid.
The GTFS transit data is now found at http://archives.sfmta.com/transitdata/google_transit.zip.