First time I start my truck in the morning I have to crack open the throttle just a little to get it to start, like the high idle circuit isn't working. If I don't open the throttle a little the motor will fire a few times and then flood out and will not start unless you hold the throttle down a ways, then you can smell that it is flooded.
For the rest of the day the truck will start normally, but after it sits over night it does the hard starting in the morning. I have changed the Fuel Pressure Regulator for 100 dollars, too much for such a little part. Could it be a sensor or the throttle position sensor?

That would be my guess the fuel pressure. It might be that the regulator did not have a good seal on it when you replaced it - you did use a new seal, right?