If not already done, replace the fuel lines.
Could be cracked and sucking air, or degrading internally from ethanol. The inside can swell shut or flake off.
Look inside all fittings, check for flow, disassemble and clean the pump. Flaking rubber from the hose, or any debris can be clogging the flow. The lower the level, the harder the pump has to work. If borderline, it falls short of demand.
If the filter is on the suction side of the pump, try moving it to the pressure side. A fine screen type filter works better on the low pressure system than a paper filter.
If there are 2 tanks, possibly the change over valve is a restriction or sucking air. Try direct plumbing one tank, see if the problem goes with the valve.