the problem with the first substance painter file
When experimenting with the bed texture files, I initially added the height, roughness and colour information on one paint layer for each texture I had created which meant that it was impossible for me to edit the height information, for instance, afterwards.
I will consequently use a non-destructive process. If your entire workflow is non-destructive, you can make edits way upstream in your process, and have the changes automatically propagate downstream.
smoothed mesh
Moreover, the model I had imported in substance painter was unsmoothed which meant that when I would have imported all the different texture files in maya they would have look deformed on the smoothed object. So before starting working again on the textures I have smoothed the mesh in maya (saving a file where the mesh preview was still available) and imported it into substance.
layer process and height information
The new process I have followed included creating a fill layer with the roughness and colour information and a mask attached to it with a paint layer where I have created the different paint brushes.
This time I also inserted the painting into a colour picker program to select the exact colours from the painting into substance.
This is the texture render so far: