I voted blue, just because my car is themed black/blue. So it all depends on your cars theme, if you are going black and red, do red but keep in mind the hazards of driving with certain colors. Doc mentioned some time ago that blue and orange were good choices not sure what he said about red.
The difficulty for footwells isn't too hard as long as you have the tools and some electrical knowledge. I can't comment on the cup holders but LBC does have a write-up on it so you can use that as reference.
For the footwells I used LED strips from
http://www.oznium.com for the cup holders I would use individual LED's.
Hope that helped kind of