I am by far no expert but I would wire wheel or sand all the rust areas paying special attention to the areas around the roll bar. Any soft spots have to be cut out and patches welded in. If you have large areas that are soft then you need to weld in a floor pan or partial floor pan in that given area.
There is a way to add body panels using a type of epoxy but I don't think it could be used for floor pans since they are part of the supporting structure of the tub.
The cracks could be fixed by driling a hole in the end of each crack then welding them up the cracks. If you find no soft spots then after you repair the cracks I would choose a bedliner and prep and do the liner. Prep is the key. I used Herculiner and ther UV protectan they make and it has held up well.
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If what doesn't kill you, makes you stronger, I should be able to bench press a Grand Cherokee by now!