Take a look at my build thread. It will give u an idea on the install process. I set up my tub so I could use a soft top or a hard top with ambulance doors.
Builds - Fj40 Daily and Wheeler build
I personally wouldn't use the factory tire carrier. Mine always rattled and I happily ditched it with a bumper carrier. The aqualu can definitely handle the weight of a body mounted tire carrier, but its a good oportunity to upgrade to a bumper mounted tire carrier like the 4plus products bumper or 4x4labs. Their are no captive nuts in the aqualu tub, so you have to use nuts and bolts. I used some of the hardware from aqualu, but since its all standard hardware I bought some stainless metric hardware just because Im picky. Their is a lot of mock up to be done with the aqualu before you actually permanently mount it. I went the extra mile on my install with a few items to make it look somewhat factory although my cruiser is not at all stock.