How can I create an isometric Machinarium style game?

I draw lots of sketchbook city scenes using loose/freeform isometric perspective. It would be amazing if I could turn these artworks into UE4 game levels with matching perspective so that the player can follow paths, solve puzzles and walk up to visible doors to “enter” new levels etc. A perfect example I can think of would be a cross between Machinarium [Example][1] and Pokemon.

Here’s a sample artwork, ignore the animation effects but as you can see I have already experimented with cutting up the different levels into separate layers.

http://cdn.owenprescott.com/wp-content/uploads/2016/07/op-IMG_2572.gif?5fcf05

My Approach:
The floor/paths are where the player would move, although ideally I would allow the player to move behind buildings (e.g. 50% opacity to objects in front). So one option would be to model the entire city in 3D using an isometric camera, however to model out my artworks would take a large amount of time.

Another idea would be a fixed isometric camera angle that shows the entire map (2D drawing as layers). I then want the player (a pixel size capsule) moving around following the paths (either 2D or 3D) with buildings etc blocked out from the front.

My main goal is an easy workflow so I would ideally like to work with image layers as a method to control player navigation. Do you have an advice on best approaches to achieve this?