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HI John.
I think I can help you out, not only am I a Mechanic, but I also own the same model Pajero, but in petrol.
But irrespective of that the system is not a complex one. It is a Hydraulic Clutch System.
Is the pedal stuck at the top of its stroke or on the floor?
What was done last time and what was the reason for that?

Cheers

John
Yes it is possible that something else has seized. Quite possibly where the throwout bearing slides along the snout of the gearbox was hurt last time. If there was enough water entering the bell housing to seize the clutch then that would have been enough to damage the snout. The snout and sliding surface of the throw out bearing should be lightly greased with molybdenum sulphide grease.
Do you have a list of parts that were replaced, if so scan them and post in your reply and I will have a look at them.
Either way It is gearbox out and back to the dealer