I wasn't to concerned about the boxes covering the lights. I figure that I will be infront of cars enough more than often when changing lanes.
As far as the milk crate, I have one, just haven't put it back on yet. Milk crates are great, especially when combined with a bungie net to hold everything in.
I probably won't paint the boxes, paint the bike though, that's not a bad idea.
Also the cases are rock solid with the bike. You shake the cases, you shake the bike. I also welded one side of the lid so it hinges and put a tab on the back side so I can lock it. Makes it totally secure.
I'll try and get more pics with up close views also.