If the problem is only happening after the vehicle sits over night but it does always start with long cranking (followed by odor etc) then we are nearly certain to be a fuel retained pressure issue... it is pretty common on this model.
What happens on these vehicles is the fuel pressure tapers down while sitting which will result in the hard starting and flooding odor two ways, either due to actual flooding while sitting (fuel leaking form injectors) or flooding while cranking due to reduced fuel pressure at initial cranking.
To verify this you would need to use an inline fuel pressure tester (hooked up via banjo bolt at the filter usually), start the engine then shut it off, and finally watch the pressure. Under normal conditions it should retain 95% of its pressure for five minutes and 80% of its pressure nearly indefinitely.
When this problem occurs you will usually see a sharp drop at key off, then progressive decrease thereafter.
Once confirmed the problem can be narrowed down (obviously verifying no leaks first) without too much effort. The first thing to do is either clamp off the fuel return line securely or remove it and install a cap on the pipe from the fuel rail then recheck the condition.
If the pressure is retained longer, then the fuel pressure regulator has failed.
If the pressure still drops, then you are down to either the fuel pump (check valve in the pump) or an actual injector leak. At that point you would want to pull the plenum and fuel rail then energize the pump to pressurize the system briefly while watching the injectors. Of course if any drip... even a little... then replacement is in order.
And of course if the injectors are tight and the pressure is still dropping, then you would only have a pump check valve failure to consider.
Now if it is not the typical fuel pressure drop issue like we usually see on these, then more investigative work would be in order... however your primary expectations at that point would be either a ignition loss or ignition/injector pulse loss. From there you would want to check the crank signal, output pulse from the PTU (power transistor unit... "ignition module"), and the ECU itself (capacitor leakage).
Realistically... it is more likely to be the fuel pressure drop off issue. That is the only one that will consistently only occur after sitting a long period. Crank sensors, PTUs, ECUs etc... they are more random in when they decide to act up and not so much on a schedule.