Rule #1... When in doubt, the FSM is wrong.
Your airbox is correct, but that damage is what happens when the airhose isn't all the way on and touching the MAF, and / or the hose clamp is gorilla'd when you tighten that clamp. Been there, broke that. Drove with it cracked for many many miles, wrapped badly in tape.
Now, on to the turbo swap. You might want to contact Papaindigo to see if he has a document outlining the procedure we followed for turbo removal in prep for the upgrade to the GDE turbo. Obviously you would not be doing the second half of the directions, but the removal parts would be quite helpful for you right now. In reference to your questions, refer to rule #1 frequently. You do NOT have to drain the AC or the radiator... Or start by removing the rear seats and all the tires from every vehicle in the area. I think the FSM adds in useless steps to everything as a way of punishing us for ever buying something they clearly did not want to sell or support.
Anyway - Once the airbox and the air hoses are out of the engine, the next thing will be to unbolt the radiator bottle from the firewall. Don't unhook any hoses yet (or ever, for most of them) but flip the bottle on its end toward the passenger fender. There will be some maneuvering with this thing as you go, but the only line you might want / need to unhook from it (just to reposition it) is the smaller overflow hose that (IIRC) comes from the upper left (passenger) side of the bottle, and snakes under some of the AC stuff. Unhook it from the bottle, clear it from the obstructions, and put it back on. That finishes your work with that, save for pushing it around as needed. For a time estimate... I can do it now probably in about 3 hours (2 hours flat was my fastest time, but that was on my own 'not-everything-stock' engine) but you are probably looking at 5 hours for the whole job. It isn't terribly complex... Just tedious.
The directions from GDE / Papaindigo will be more help, and I'm also available for tech questions if you have any. When you PM Papaindgo, he can give you my number - I'd do it now but my laptop is just about out of power and so am I for tonight.

Good luck, catch up with this as it progresses.