The connection to the top of the master cylinder is as George put it a vent. The diffs, the master cylinder, the transfer case and the transmission all are vented together for deep water fording. Have a look underneat than you can follow all the lines to a central point from those vents if all the hoses are still there and intact.
THe hose from the top of the fuel pump/vacuum pump is for the vacuum wipers, and goes inside the cab to the wiper switch/valve and on tot he wiper motors.
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