I'm playing v3, and I have every item except the eye and the purple key.
How do I open the gate into the blue watery area in Deep Halls?
What am I supposed to do in the Yurees' Cave?
In the Halls of Souls, there's a screen with a blue key door & red bouncing enemy. It has a red light that says "Activate? >>" but doesn't do anything. Is this normal?
In the Halls of Souls the switch on the screen with the blue door and red bouncer activates something on a different screen. If you backtrack to the screen with 2 gray bouncers you will see a passage leading down that was not open before. You could get the climb power down there if you didn't have it already. You should go back to the start of the area and leave, because you can't finish this section without the eye power.
Edit: Since I'm playing it now, I'll answer the other questions.
There is an obvious screen where you can get a peek at the secret aqueducts area. The gate is actually an immovable grate. There is another entrance elsewhere which is ridiculously well hidden.
Yurees' Cave is impossible without the eye power.
I tried to find a "Let's Play" video to suffice as a complete guide, but there don't appear to be any anymore.