A good first step for an owner of an MEFI (Marine Electronic Fuel Injection) engine is to do an internet search under the terms "Pirate 4x4 MEFI4". This will lead you to an excellent article that explains just how MEFI controls work on an engine. It will also give you pictures to identify just which controller (ECU) you have on your engines. Once you have an understanding of how the controller functions, trouble shooting becomes much easier. The article also has a link to a diagnostic manual for the MEFI4, which is one of the most common of those engine controllers. Earlier models lacked some os the features, and later models have some additional capabilities, but they all use pretty much the same type of sensors and the same operating principles. So the manual is useful to all. If you print it, go double sided, it is long!
Once you have read those, you will know just what to expect from a scan and how to interpret the data. But because you will understand the operating principles, you may be able to find the problem without a scan if you don't have ready access to a scanner. The actual start up problem you are experiencing is most likely caused by a lack of response in the Idle Air Control (IAC) valve. This is a stepper motor controlled air valve next to the throttle plate that does what you now have to do manually on that engine. So one place to start would be to swap those valves between the engines. Or the problem could be the computer that controls the valve is getting bad input and therefore not telling the valve to move properly. This most likely would be the temp sensor (as suggested by Mark) or the Manifold Air Pressure (MAP) sensor. All of these are very quick and easy swaps. I believe that if you swap these three (one at a time, please) you will likely find the bad actor. If not, the documents will point you to other possibilities.
Good Luck,
CaboJohn