Get the schematics out and trace connectivity to each pin on the clock chip from agnus or wherever it's supposed to connect. It could be the variable cap affected by corrosion as well - you could probably take one from a 500 memory expansion.
Good idea. As a cross check, chip pins are numbered counter-clockwise (looking down on the component side of the board) around the body from pin 1, which is the next pin after the notch.
You could confirm power to the chip while powered up.
You are certain there is no moisture remaining under this chip? Check continuity from pin to pin and cross check to the schematic.
EDIT:
With a scope or possibly a logic probe, you could test for a pulse train out of Y800.
If you replace U801, use a solder sucker AND solder wick (Radio Shack) to remove as much solder as possible. It would hurt the MB the least to gently snip the old chip out and then remove each remaining pin individually. When you install the new one, align the notch. Sparsely apply solder to the pins on BOTH sides of the board to ensure that all the layers in the MB are connected to each pin.
It would be a shame to waste the work you have in this board already.