I'm tempted to try soldering the lighting units in place, although at the quantity you are thinking about that's not gonna work.
I'm not sure that would help. The contact from the truck to the brass strips that run the length of the train acts like a leaf spring above the truck to allow it to follow track irregularities. The truck/spring joint is the first problem area, and since the truck has to pivot, you can't solder it (short of soldering wires directly to the truck). Then there's the L-shaped bit of brass that rests atop the spring strip. You probably couldn't solder it because it's located inside the floor, but if you could it might prevent the spring strip from flexing as the truck moves, which would be a problem. Finally there's the connection from the L-shaped strip to the lightboard. You can solder that, and I did on one car, but it didn't help.
Wires direct from the truck to the lightboard could work, but would require a bit of surgery on the floor to allow them into the car with enough extra length to allow the truck to pivot. That wouldn't be my first choice for a solution.
A capacitor will solve the problem, although you probably need to add a few other bits. The attached circuit diagram shows a circuit that worked for me. However, I've only built one so far (still working out a good way to put the bits together that I can do quickly). I
wrote this up on my site if you'd like more details.
I've never installed lighting in a double-decker, to get back to the original question. However I do have a few E231 double-deckers, and just opened one. I don't know if the 100-series is built similarly, but I expect it would be. In mine, the diffuser strip is built into the roof, rather than being added using the part in the kit, which allows it to follow the curve from the end (where the lightboard is) to the middle. And the floor of the top section has most of the aisle between the seats cut away. The light reaching the lower part will be a bit dimmer, but since the LED shines down the middle of the diffuser, it may work fairly well.