First reaction? That shed has got to go!! Why the previous owner thought moving everything onto a plywood floored base - and then cut away the support joist under it, was a good idea is a mystery for the ages! That filter alone is a large amount of weight on rotten, unsupported plywood!
Likely the concrete pad is still very useable. Perhaps you can get a few pics of it by holding your phone camera under that side of the shed, or via the hole in the floor.
While the electrical box seems to be in pretty rough shape, it appears that you would not even need to disconnect anything for the shed removal.
The SWCG control box would need a post or similar afterwards to be mounted to.
You've already "mastered" plumbing, so redoing it all to get rid of that Rube Goldberg mess of piping would help a lot in optimizing the flow of water. The challenges would be getting new unions and a flow switch where the 90's are so close to the filter, SWCG, and the pump inlet.
Others can better address whether to replace the filter, or not. Although I might tend to lean to the "or not" side of the question.
Ditto on the pump, especially as a new one would likely mean another slight redo of the plumbing.