Thanks for the responses. It should be noted this motor is brand new. It is a warranty replacement for a 2012 that Tohatsu was unable to repair. So yes, this is the second brand new Tohatsu that has problems.
I know the first piece of advice is to bring it in to be looked at, but the dealer in my area is closed weekends, and my taking an afternoon off work to run a boat 30 miles up the road for drop off and pickup is much more expensive than my doing little inexpensive fixes myself. Of course, if those fixes don't work or cost more than a few bucks, I will have to bring it in. But until then I figured I would just pick some brains on here

.
I had enough spare boat stuff laying around to change everything from the motor connection back, including the fuel tank, and that made no difference. I also keep a spare fuel pump for every motor I have ever owned, so I changed that out too and it wasn't the problem.
Basically, if I go through the process of "force feeding" the fuel system as per my service manual, it runs until you stop once or twice. But, once you shut it off for 10 minutes or so, then crank back up the motor runs a minute or two then dies. Sometimes you have to stop a few times before that happens. And, when it does happen, the fuel filter under the cowl is half full of air as seen in the photo.
So my question is since the fuel pump is new, and the primer bulb is also new, and both have check valves, doesn't the air in the filter almost have to be getting into the system from between those two components? If that is most likely true, then there isn't much there. A couple o-rings on the filter and a quick connect that I can just eliminate with a splice fitting.
And Guru, the following error codes are present. When the dealer installed this motor they said they couldn't get it cranked and thought the problem as a faulty connection at the fuel tank. That definitely wasn't it because I put a straight fitting on the tank so there is no disconnect. I don't know if these codes are from them installing the motor and not clearing them, or from the fuel system running out of fuel multiple times. But the Faulty FFP code is erroneous in my simple minded opinion, because as long as I pump that primer bulb I have no issues. If the FFP was bad or malfunctioning, it doesn't seem like pumping the primer bulb would make a difference.
Light 1, 2, 3, RPM
off, off, steady, 5500 - Faulty #1 TPS
off, off, steady, 6000 - Faulty #2 TPS
on, off, on, 5000 - #1 TPS Power supply high
off, off, steady, 7000 - Faulty FFP
blinking, off, steady, 5000 - #2 TPS idling position error
off, off, steady, 5000 - Faulty CPS
Thanks guys, and sorry for the lengthy post.