Okay, let me think about that. Is there any possibility you can start the engine out of water and see if the same thing happens? I was thinking this is a two-engine boat thus swapping from left engine to right engine for example.
It's very important to always change spark plugs when experiencing this type of issue, I'm sure you did that already just mentioning it.
If the engine stalls completely and quits (falls on it's face), that's most often due to it runs out of fuel. This leads to checking the fuel lines and all fittings for leaks but I'd bet already your mechanic did this. Any little leak will allow too much air to enter and fuel starvation occurs (pretty common). Two most troublesome places are the fuel/water separator bowl gasket and the fuel shutoff valve internal o-rings. As a quick and dirty method, I usually remove the fuel filler cap to avoid pressurizing the fuel tank then disconnect the fuel line from the fuel pump inlet and blow low pressure air (less than 5psi) back towards the fuel tank while listening for leaks. Under normal conditions, you will hear air bubbling up from the bottom of the tank pickup tube much like a fish tank airator and see or hear no leaks in the various fittings. Also you may shut off the fuel shutoff valve and the pressure must hold.
Sometimes debris from over the years can lodge in the fuel valve and partially block fuel flow, causing fuel starvation. This can be avoided by temporarily bypassing the fuel valve.
Since we haven't heard from [MENTION=41828]Minnetonka4me[/MENTION] yet, let's concentrate on this coil.... I need to confirm which type is fitted in your boat, since they're not cheap and probably even more expensive in New Zealand then I'd imagine.
Aside from plug wire length, there are basically two types of coils used on this era of engines, single and dual type coils. maybe your local dealer has an alternative in stock and your mechanic can work with to swap plug wires as necessary..
Specifically, in the 1st case there's a single coil design that fires two spark plugs, it has terminals on it for two plug wires. In the 2nd case there are two separate coils. This 2nd case doesn't seem to match the drawing I see from the drawings of your boat, it appears you have the single coil? This would be consistent with NO SPARK BOTH CYLINDERS, b/c if the coil breaks down both will drop out.
(It makes a huge difference, need to get this basic difference correct!)
BUT!!! Based on there are two separate part numbers, this indicates two separate coils. Thus I'm confused by that.
Can you confirm your boat has the two separate coils system or single coil? This little detail is important to the entire detail of the electrical system in many ways, there are major electrical differences between single and dual coil system thus this is the one single most key point for many of the electrical parts, including the flywheel type.
1997 787 XP for example, shows just a single coil, p/n 278001254 IGNITION COIL You can see, this single coil fires both plugs. If yours is also the single coil configuration, I believe this coil should be able to accept your longer plug wires, and/or replacement wires if required.
Point I'm making is, I'm not convinced any 787 coil is applicable depending on this major detail, we need to confirm which type of ignition system your boat was configured with, for this reason.