Don't want to sound stupid but I'm not sure I understand about the pavers and the gravel. I visualize filling the cut area around the pipes with gravel and then laying pavers on top.
I am trying to figure out how to raise the pipes and valves and then connect to the pump
I was also thinking of filling in the cut out area with gravel and using pavers or patio blocks if you needed more slab space.
You could raise the height of the pump with patio blocks. That would raise the height of the pipes feeding into it from the manifold. You could also make the pipes a little taller coming out of the ground and use 90 degree elbows to connect to the pump, similar to how the line from the pump goes into the filter. The current set up has everything butted together so tight it would be difficult to saw into the lines to make repairs, unless you have a power reciprocating saw. I think you could also push the pump and filter back a bit after you pull the heater out and put the valves on the horizontal run of the pipes.