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Thank you for allowing me to assist you, my name is Joe and I will be happy to assist you with your concern today.
If the engine and distributor is correct per application then the firing order and timing will not be different then what the motor calls for, the procedure for setting the timing would remain the same. Now if something is different then it'd just be a difference of firing order and the timing would/should still remain the same, any changes would mean you would need to locate what year/model the ignition system is from if that was also changed, otherwise simply swap the old ignition system from the engine being replaced to the replacement.
Hopefully I have understood your question correctly, if not I do apologize.
Thank you!- Joe
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I see, I think what you are saying is that this vessel had a different motor in it before (not computer controlled as an example), this computer controlled motor will control timing however the base timing must be set, you did correct with tdc setting of the distributor but you still need to set the base timing and if you can provide the complete model number I would be happy to locate the timing specs for you.