I don't think you will see any increase in fuel economy if you take the tool box off your trailer. Remember how much quieter it gets in your car when you tailgate a tractor trailer. The same thing happens behind your vehicle but on a smaller scale. The increase in drag is mostly (at least for me) due to the boat being wider than my car. So, my car has not moved the air out of the way yet.

I don't think a couple inch difference in height of the trailer will increase your fuel economy either for the same reason. Most of the drag comes from the boat being wider than the tow vehicle. Your best bet would be to dissassemble to the boat so it can fit within the width of your tow vehicle. Then you will have better fuel economy.

My 2 cents