We are doing the upstream disembarking at 0900am, do we have time to get to catch a 1040am train from Chongqing West Station?
Unlikely. Best to allow a travel time of 1 hour, plus 30-40 minutes to get into the station and to boarding platform (that assumes you already have your train tickets in hand). Then the disembarking may take the better part of another 30-40 minutes. If you're heading for Chengdu, the next train from Chongqing West at 11:49 would be the one to take. Or go to Chongqing North station which is closer to the port, and should be able to catch the 11:16.