Is that a steel braided line from the pump up to the filter fittings? Looks like you still have to put your rad hose and thermostat housing on. Do you have the rest of the components attached up front? You might want all that on before routing the fuel line.
I had the same manifold with a spacer and it had clearance. I now have an RPM manifold, there's just enough clearance to have the filter on the inlet tube.
Like Bob says, you may be able to slightly bend the inlet tube if it can't be loosened and rotated up a bit to eliminate the fitting chaffing on the manifold.
