I'm more of an expert with the old classics, and I am not real sure of the nomenclature of all the parts on the SN95 but I do own an 03 Mach1, and when I took my K&N filter out to clean it, I disconnected the air tube from the EFI and tried to start the engine with it disconnected so I could spray some cleaner in there. Anyway, it acted just like you describe yours as acting. Make sure the tube is connected all the way from the filter, through the MAF and into the EFI.