Would be an awesome project
My approach would be to remove everything from the chassis forward and worry about the body panels and the under the hood accessories after the engine is in. Everything will have to be fabbed (including the engine mount) so you might as well get everything out of your way.
Also, remove the coil springs and refab everything so it’s compatible with a set of springs which are available at different rates. Or go coil-overs but obviously make sure you can find a range of coil-over springs at very high spring rates.
The transmission tunnel will probably have to be modified too. If you’re going manual transmission, the New Venture 4500 (NV4500) is one of the best you can find out there. If the 7.3 comes with a turbo, its usually located at the top and the back the block, and offset towards the passenger's side a little, which means you'll probably need to relocate it -- not only for clearance, but easier maintenance down the road.
If the Explorer is a 4wd, swap the front axle for a 2wd system (either TTB, SLA, or a mono-beam 2wd). The axle (especially for the TTB or mono-beam) might also need to be moved forward depending on where the engine ends up – not only to clear the oil pan or whatever, but also for better weight distribution.
Of course the 8.8 will have to be swapped out for either the Sterling 10.25/10.50 or the Dana-70 – at least.