I have a yamaha 200HP 2004, might be a similar set-up, check the tilt sensor is operating as in lift engine on tilt and move the sensor arm to check if working, if it is also check the small bracket the arm pushes against as these can break or can move, also check wiring.
I had the sensor go wrong once and the bracket break once, different times, both parts replaced at different times, ive also had the bracket work loose which needed re adjustment and also after some one did some work on my engine they must have tilted it up so high the sensor arm went the other side of the bracket and hence I had to re adjust the bracket yet again and it is a pain.
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