I suggest you re-visit that in-tank filter. Does it have the original sintered balls filter? Those things are famous for getting plugged up and restricting flow to the carb, so the carb doesn't get enough fuel to replace what was burned--then it runs out of gas and dies.
You say it has good fuel flow, but does it? Another famous problem is the filter gets plugged mostly in the bottom half. So, you get plenty of flow when the tank is full, but not enough when half full. ALSO, consider the fact that the motor as it sits on the transom it possibly is off-level as compared to how it was sitting when you checked the flow. In other words, the fuel level might be lower AT THE FILTER.
These are common problems. Check it out, don't assume.