If this is still an open topic, I'd like to share my thoughts. I think it's a good project. I like the idea with the roof hiding the VUK ramp and as well the discrete "multi ball ready" light.
In my opinion LW3 is one of the pinballs that matches very well to LEDs. Though, why not making a PCB for the 3 lamps(Victory, looping and double jackpot) and hide them as well behind a window?
For the 2 flash lamps I used two LED strips with 3 LED each instead of the flasher bulbs and I just stuck them into the house. Works pretty well.
So if you redesign the house, why not get rid of all that ugly rivets and replace the bulbs?
Maybe you can also design in stable plastic holders instead of riveting the original brackets at the bottom?