I have not done one of these, but looking at your pictures a couple of thoughts come to mind.
I think you will have to do away with all the spring contacts on the smoke unit boards and rewire all the shell lights using 2 pin plugs. Lots of work but doable.
Basically on the smoke units you want to cut all the circuitry except the two resistor pad, and put them in parrallel. I would dremel the unused part of the boards off altogether. PS-2 boards can run two smoke units in parrallel.
If there is a constant voltage board that controls cab lighting through the spring contacts, you could retain it. In this case I would just cut the smoke board traces along the outside of the board just adjacent to the pair of screws by the air intake hole. This is referring to your second pic. This will effectively isolate the resistors from the rest of the board.
The ditch lights should be programmable so that they either stay off or work automatically through the PS-2 programming. I don't know if MTH has a specific DDA40X sound file but I would guess so.
The upgrade kit comes with a manual smoke switch that you mount through the floor. You use this to control the smoke in conventional. In DCS it is controlled by the PS-2 board.
This will be a challenging upgrade, and may not be the best choice for a first attempt.
But it is certainly doable.
Rod