I went through the crypt and dropped down to the dock and asylum. I swim down the main channel and the three side channels, jump out of the water, and kill everything, but I can't find the upper chamber with Scabban. I go up and down the stairs, and found an elevator, but can't seem to find my way forward.

From the walkthrough:

Swim along the canal to the large north channel and go north to the short east ramp into the First Asylum Room.

To get to Scabban’s Room go up the stairs, turn south at the corner, then go west at the mummy case. Follow the walkway west and then north. Go around the "U" (west/south/west) and continue to the base of the wall stairs. Go up the stairs, turn slightly west then go south and east along the wooden walkway. Take the stairs down at the corner, turn south then go east to the stone bridge. Cross it and go east, south and then west up the ramp. Follow the only route possible to the Poisonous Fountain Room and take the other east exit to Scabban’s room.

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Rick
Beginner's Help, Hints, Walk-Throughs at The WWHAP