Re: please help engine starts and runs but will not shut off
OK, it's 2 o'clock and I have just come in from greasing a winch (not a boat winch, one of these)
I was thinking about your problem... Engine and instrument wiring is not that complicated, in fact it's quite simple (it has to be, that's because most boat mechanic are .... we'll just leave it at that

). By now you should have downloaded the manual Don kindly gave you the link to.... Go to the wiring diagram for the engine (page 4F-3). That is ALL the wiring on the engine. If I was faced with this problem the following is what I would do...
Disconnect/isolate the battery, unplug the main harness connector and deal with the engine as a separate entity. This, by the way, is my standard method of attacking any problem (expect women). Divide the whole into smaller, manageable sections, deal with each one in turn, problem solved. The signature of one of the other members here has words to the effect of 'finding out what IS working is as much a part of the troubleshooting process as finding out what is not working'... Very true and useful statement. Often you can be chasing a problem that is caused by 2 faulty parts.
Ok, engine entity. Check that each wire is connected to the right place, and that its colour is correct. Check that each wire is not shorted to ground or to another wire. This could take you a few hours, so I would print out the diagram (a few copies) and take them up into the boat with you. Tag each wire that you check and mark it off on the drawing. On the drawing each subsystem on the engine is outlined, I would do the checking by subsystem. Once you are happy that all is correct and right on the engine, reconnect the battery and start to check various points for power. Points that SHOULD have power are the main terminal on the starter, the orange connector on the alternator, any red wire and any red/purple wire. NOTHING ELSE SHOULD HAVE POWER. Check the coil terminals, they should be dead.
IMPORTANT POINT: Check and ensure the engine grounds are solid, clean and tight, and in the right places....
That should have the engine wiring cleared and set. Once you have all that done let us know....
One more point... Whenever I wire a boat I treat the engine (and engine instruments) as a single, separate system to the rest of the boat wiring. Accessories and ancillary equipment should NOT be wired to the engine system... The only thing the 2 systems should share is the battery and the battery isolation switch....
Chris........
(This process may take a while, as we are about 12 hours apart)