I'd still say that after all that fuel line business you could have dislodged some crud that's stuck in your FPR. Like you say too much fuel or flooding can be caused by your FPR being stuck open which may seem as though your fuel is fine and is getting through but is there too much? Hence the sitting overnight and then starting again easily once it's not flooded? Check the easy things first.
Of course there could be a few different things going south on you. Old electrics, loose wires, even a loose battery connection could all cause your symptoms.
Intermittent faults are always the most fun to diagnose. Be sure to let us know how you go.