Hard 'Cool-Cold' Start GT-40 EFI

I've seen several posts where the issue is stalling/not starting after several hours of use. Mine is the opposite. Last Monday morning my wife and i headed down to our 99 SN GT-40 EFI. It was the first 'cool' morning as the temp was around 54 degrees. The boat has started flawlessly all year - first quick turn of the key. This morning it acted like it had started but then would stop after 2-3 seconds. Several attempts, same outcome. Tried holding the key longer - same result. Finally got to it start by pumping the choke (probably not suppose to - have never done it before. We went out, got our ski runs in, came back to the dock, turned off - then tried to start and it started right away. 54 is cool, but not cold.

Any thoughts?

With your EFI, the only thing you do by pumping the throttle is open the throttle body which does let in more air.   With EFI this is normally no help starting and actually messes with your computer while it is trying to focus on your start up.
If it is helping your engine start I suspect you have a fuel leak, some flooding going on and the extra air is helping at start up.
Otherwise, Ken is correct and you are not helping by moving the throttle while starting.
Easy to check to see if your injection is leaking.
Hook up a fuel pressure gauge to your fuel rail.
Turn your key on and off a few times to pressurize the system. Wait 2-3 seconds with key on each time for the pump to shut off again.

Now watch and see how long your pressure holds. There is a factory standard established, I don't remember the numbers but if you do this and see your pressure quickly dropping off you have an issue. It should hold pressure at least a few minutes and then slowly drop off.
If pressure drops quickly you have a leak, it could be the pressure regulator or an injector or two failing.