Sounds like they are still a horrible piece, albeit much better than the previous horrible piece!
Don't trim anything until you have it mounted correctly where the dome light is which pulls it up into shape. The original dome light mounting studs will tell you the height that the panel and light base sit at when correct. An original board could be pushed up and down here on the studs to see the rear of the light, then come back down firmly as it retakes shape. If you have it mounted correctly on those 2 studs, it will tell you where in the overlap it needs trimming.
I don't know if the boards have the same 6 side tabs that insert into the roof or not. I'd be doing sun visors last, probably just clearance holes need adjusting. The other trim panels simply overlap, board is likely oversize, given the overlap they had some room to work with that would allow it to not be trimmed anywhere.