noticing that during the brine fill cycle too much water is being put back in and level is above salt.
Fluid above the salt doesn't itself signify much since the salt that was dissolved during each of the manual regeneration cycles, will have caused the remaining salt level to become lower. You didn't specify if you added additional salt.
To ensure a consistant quantity of water entering the brine tank each cycle, the Fleck 5600 utilizes a timer and flow rate restrictor. Regardless of the amount of salt remaining, the same quantity of water should be entering the brine tank each cycle. We usually recommend refilling the brine tank with additional salt when the remaining salt starts to be submerged below the fluid.
When there is an actual issue resulting in too much fluid within the brine tank, that is often the result in brine not being drawn from the brine tank. You didn't indicate if brine was drawn out during each manual regeneration cycle, and you didn't mention if the safety float within the brine tank was being lifted so as to stop water from further entering and overflowing the brine tank.
You also didn't clarify if the additional manual regeneration cycles restored soft water delivery to faucets.
Since the issues occured immediately after replacement of the well pump, perhaps the pump installer bypassed the softener to prevent sediment or other debris from entering the softener.
Suggest 1st inspecting the bypass valve(s) leading to/from the softener. The bypass should allow flow to/from the softener. If equipped with a Fleck plastic bypass assembly, that will typically include two separate valve handles so both handles should be parallel and inline with the direction of flow.
Some installers do not utilize the factory bypass assembly, but instead will plumb in 3
individual valves as a bypass. Again, the two valves leading to/from the softener should be fully open, but the 3rd valve (bridge valve) that will allow hard water to bypass the softener, should be fully closed.
