First thing —> Fan-bloody-tastic. Night and day. Sounds like you have the story worked out and pretty much the shape you want it in. What an immersive experience! Congrats! 
Now to some specifics:
a) Vocals are not clear, and sound smeared in with the rest so much that it is hard to make out the words.
For vocals, if you want them to be understood, you do need to leave some space around them, typically by:
__ i) Sculpturing other things around them. If you want guitar up loud to be driving things along, you need to use ducking or automation to drop the notes down, including the one immediately before a vocal line starts, and fading back in at the tail of vocal lines. Guitar notes during significant vocal pauses in the line can be brought back up.
I typically set the vocal level and sculpt everything else around them. But then, our music is sparse. Your mileage many vary!
__ ii) Don’t apply the same effects to them that you are using heavily for everything else. Perhaps use a different reverb (plate) just for them so the quality of their space stands out from the rest.
b) My opinion, but the first time the female vocal appears, I suggest starting at the centre, just so we know that she is important. Then you can move her around to show her confusion.
c) I feel the male and female vocals are meant to be equal, but the male is more out from the centre and mixed back. Sort of takes a bit away from the beautiful blending of their short duo lines.
Again, beautiful! You are close, and may not need much more to be getting something out the door. I am impressed with your creative producing skills. They will carry you into areas others could only dream of going!
One thing I learnt from tech writing. If a reviewer mentioning difficultly with something, it usually meant something wasn’t quite flowing right, so I would usually make a change, mostly minor, but it improved the flow.
Just because the notes may be right, does not mean they sound right. Here, it is not the overall note pitch, but the flow of the pitch during the note. It sounds like the note pitch is wavering a bit too much in the wrong way.
Cubase has some neat stuff to change tuning. You can chop the note up and flatten variation in a section, or change the slope of the pitch variation. Might be time to learn a couple of Cubase tricks?