of those options. i would choose back up lights, and the box. i put backup lights on mine when i did the led conversion and i love them.

I think you mean Cadmium rotors, and Stainless calipers. This is a great upgrade, IMHO.
Also, go with the box. You are right on keeping stuff in there. Chocks, jack, fluids, spare parts.
1) Make sure the box is mounted HIGH so if you get to a ramp that is really flat/shallow, you don't have to dunk the trailer so far that the trailer box gets wet.
2) Also, make sure the electronics for the EoH brakes are mounted HIGH as well, for same reason.

The ONLY thing I don't like about Manning trailers is that he typically uses wood blocks covered in carpet for the V-bow stop. I don't like this. It's too harsh on the boat. The grey rubber blocks that Myco uses are better. Make sure you either source these for Ron, or ensure he puts them on your trailer.
I use a spray wax on my rubber V-blocks before I retrieve the boat (which I keep in the took box). I spray the rubber V-blocks down with the wax before retrieving, and just wipe the wax off the boat. It works slicker than frog snot, literally.

Also, I'd go with two spare tires. You can never have too many; especially if you are going to take long trips. If configured correctly, they can be on either side of the V-block/bow stop and act as additional guides to put the boat on the trailer. If you want to go cat's ass; you can have two spare spindles mounted with hubs full of bearings and everything so if you blow a bearing, you can slap on a new hub and be on your way in minutes.