Clean it, and put new plywood down, and keep it. Great place for lawn equipment. Doesnt have to be perfect. The roof is already done for you, so a few sheets of plywood, and some scrubbing, makes it pretty much usable. It would have been nice if it could have been raised up to get it right off the ground.

I can't give as good advice based on pictures and what you tell me as I can after personally inspecting the building but i'll help as much as I can under the cercumstances. I don't see any plywood,would you care to show me some before I tell you it should be replaced? See what I meant in my first statment? The building can be elivated but agin,that require's someone on site that knows how instead of free advice by strangers on the net that never laid eyes on the building. Now,perviding there is a new properly installed roof,I can tell you someting without seeing in person. Us an airless or hvlp sprayer to coat 100% of interior shown in your pictures with exterior stain killer primer. I prefer oil base Zinsser Cover Stain or Kilz Premium. Not as effective but easier clean up you can use Zinsser 123 or Kilz Premium. That will cover all the stain and give you a better attitude ever time you go inside and alows painting interior without bleding.

He said our best bet would be to replace plywood where needed because it has a new roof.

There is no plywood to replace. The only bit of plywood is the roof gussets (connection plates) on the gambrel roof framing. The siding is real board & batten.

The irregular bottom edge may be weed eater damage more than anything.

Agreed that the black stuff is water stained wood. Not mold.

And the other thing the contractor told us was that the way the shed foundation is it will impossible to just lift it...

Not sure that I am buying this. It may be impossible for 'this' contractor to lift it. Ask the previous owner if the shed was built in place and for any info that he can give you as to how the shed is anchored (if it is anchored) and what it is sitting on (foundation). Or get a shovel and inspect.

If you want to remove, lighten the water stains, you can use a household bleach solution or a heavy hitter like oxalic acid solution in a pump up garden sprayer or perhaps a hose end sprayer. Keep the doors open after cleaning and run a couple of fans to increase air circulation until it is thoroughly dry.

And, yes, the shed is worth saving. Has a new roof and is far, far from being a goner. Getting it farther up off the ground will greatly extend its life.

Be sure and caulk around the floor edge inside to prevent water from entering under the jagged exterior.