Hi Ben, great work a really impressive job done, when you said you were waxing the underside, is that the waxotl stuff in the cavities etc? I'm at that stage with mine and looking for the best thing to use. I've stone guarded the underside and painted it the body colour, just looking for the best route to take.
When choosing a wax for box sections, you need to find one that creeps well so that it will flow as far as possible and then inject is from as many places as possible.
I use a wax by Wurth for this and it's easy to get through coverage on inner sills and in/around subframes etc. I keep pumping it in until it is dripping out from everywhere.
If you want to coat external surfaces, then you want one that doesn't creep so much as it will just run and drip off everywhere.
For this I use a wax by Optima which comes in an aerosol and sprays on nicely almost like a coat of paint and is great for applying to the floors underneath as it sticks well and dries into a stiff skin which doesn't wash off.
That's about all you can do and as long as the sealing up and stonechipping is done well, everything should last well.