Filling in the holes in the engine bay is just a matter of welding up the holes (small ones with just welding, large ones with pieces of sheet metal). Grind down the welds and use a thin amount of Bondo to make the area perfect so that you can't tell that the panel has been modified. I didn't do the work personally, so I know I am leaving out a lot of details. As for relocating the fuse box and cleaning up the engine bay, you just need to take your time and be meticulous. From the time I decided to clean up my engine bay I have constantly been on the look-out for things that can be relocated to a less visible location and for things that aren't needed. Example, every connector that I saw going to nothing was cut back and capped (folded back and heat shrinked or used with a twist cap). I've hidden wires, traced unused wires to their source, including through connectors, and removing all traces of the wires ever existing.
Thank you very much for the compliment, it's been a labor of love and I'm very proud of what my Supra has been transformed into.