Trouble staring in morning or after sitting for long period

It sounds like the fuel system for your 2005 Pontiac Bonneville is loosing fuel pressure while sitting. The best way to confirm this would be to connect a fuel pressure gauge, the gauge should hold pressure after the engine is turned off. If it does not, that would indicate a leak which would require further diagnoses. I would doubt very much that is problem is being caused by the fuel filter or the catalytic convertor.