Yes if ever needed you could start your engine like that as the wiring plug connector will be the same right up until 2005. Staring the engine that way is a good test to help eliminate the helm electrical components or connections as being part of the no start issue. Since another ECM powered up the fuel pump by turning the ignition key on, you shouldn't have to jump connections like that at this point.
Also since you had no spark while cranking with the other ECM, lightning strikes typically tend to damage the Crankshaft sensor which would not allow any signs of spark by not sending any reference signals. Your RPM gauge should be moving to around 350 RPM while cranking....The RPM signal basically starts at the crank sensor.
Search online images, 'boats hit by lightning damage' to see if your boat appears to have close to the same type of damage...
http://www.bing.com/images/search?q=...mage&FORM=AWIR
Your engine serial number is not visible on the flame arrestor cover so you may want to try looking for them just above the engine starters on the starboard side. The tag should look like this,
Your boat, engine year models/serial numbers were pretty close to a transition time frame for parts changes so in order to find the proper part numbers without guessing, you'll want to find the serial numbers if possible.
Being that you have the 555 ECM's, there's only one company that I can recall that offers testing and some repairs only if possible for this design ECM and that is Wipple Superchargers. Other companies are setup to repair the older MEFI style ECM's which won't be of much help to you. You may want to try calling them back to see if they've been successful with repairing lightning strikes but they may need to open the ECM up to see the damage though.
Another option would be your boat insurance may cover all the repairs.
Keep us updated and good luck.