Just a few random thoughts...
The pod may be modular, but that doesn't have to mean the entire pod gets swapped out. Maybe just the internal sensors or whatever get swapped out via those side panels or some removable panels on top.
For the turbolift, there's no reason the car itself has to be perpendicular to the other decks when going thru the pylon. Maybe it rotates to where it's top is pointing towards the front of the ship. Or maybe there's just a 0G tube thru there. (I keep picturing the tubes from Futurama!

)
And the windows, I wouldn't let their location limit you. Maybe it's an extra tall deck with multiple rows of windows? Personally I like the idea of non-standard deck heights, especially since real-world ships (other than cruise ships) rarely have two decks the same height, mostly due to machinery and space constraints.
But, this is your build, and I'm looking forward to see how you make it work!