I would run 50x50x2 rhs from pillar to pillar on the outside under that lip at the top rails, with the rails notched for it to fit (not the rhs notched for the rails). I would also put a 1.2 - 1.6mm plate on the pillars from under the lip down to the sill so you have something to weld the rhs to and it will spread the load down to the sills. I would redo the pillar corners with 1.2mm and curve the corner and then link the sills 90degrees to the bottom rails with 50x50x2 rhs. I would also extend the bottom rails forward on an angle to the sills, joining it atleast halfway along the door opening, using the 50x50x2 rhs and another spreader plate on the sill where the rhs will be welded.

The rails themselves are double plated from factory where the bottom rails meet the top rails, but with leaf springs the back half of the rails will be under load and are probly flexing now. The easiest fix will be to sleave it internally with more 50x50x2 rhs and weld it up. I would also cut out the 3 crossmembers and put in 2 good 50x50x2 rhs crossmembers, one where the back one is already and one directly inbetween where the other two are right where the rails all meet up but forward of the diff. (use shorter shocks and mount them off the rails)

Is all this enough for the engineer? Who knows, as you have cut alot of strength out. The engineer might not even think it needs any of this, but they might also say it will be easier to use a chassis from one of those little mazda utes.

No doubt you will want the tray as low as possible with wheel tubs cut up into it, but I would put it the same height as the bodylines on the doors etc.
Its definately different and good to see. It may take time and alot of work but it will be good in the end.

have a look through angry tanks pictures, lots of good strengthening stuff done to his ute

Looks to be the stock rails with the floor cut all around it.
What has the engineer said is required to bring the strength back?
You do plan on strengthening it dont you?