Hi Jeff. I am analysing the last log you sent - 10-3.
I can see you have RC1 reversed - steering. You just have 1 rudder on this boat right? When in Manual mode do you have the steering stick (whichever is mapped to channel 1) reversed? If so your setting is correct. If not your setting isn't correct and needs to be changed. Think of it like this - when your in Manual mode ArduPilot isn't involved. Every input you make simply goes straight through to the motor and rudder. When you steer left if you notice the rudder goes the wrong way then you reverse it on your transmitter right. Now, when your in AUTO mode your transmitter isn't involved. But ArduPilot also needs to know that the rudder is reversed so you need to make the channel reverse setting in ArduPilot. Make sense?
Your RC3_DZ is 0. This isn't a good idea - best to leave it at 30. The ardupilot uses this value to know when the throttle is "neutral". Without it ardupilot might continually move the throttle to try and hit that 0 number.
Your RC3_TRIM is 1556 - that's a little high but no biggie.
LOG_BITMASK is 3950. That's not a log of logging and is going to affect our ability to diagnose the issue. Any reason you don't leave it at the default of 65535 so we get everything logged?
Your FS_THR_VALUE is 1100 whilst your RC3_MIN is 1106. That's a little too close I reckon. You should be able to drop FS_THR_VALUE down to 1000. Note you don't have the FS_THR_ENABLE set so its not being used - just thought I should mention it whilst I saw it.
CRUISE_THROTTLE is 52% and CRUISE_SPEED is 1. This is telling ArduPilot that you need 50% throttle to do 1m/s. Is that correct? Try out in manual mode and see how much throttle you need to do 1m/s and then set CRUISE_THROTTLE accordingly. This setting helps ArduPIlot do the math better. Not it won't affect navigation.
Your BATT_CAPACITY is 33020000. That is a very big number. Is it correct?
Your ARMING_CHECK is checking for GPS_configuration, LoggingAvailable, RC Failsafe, GPS Lock and Compass.
And your ARMING_REQUIRE is set to 0 meaning it will boot and ARM (you have no safety button I see) regardless of what the checks say.
Your AHRS_ORIENTATION is set for 180 degress. So the pixhawk is point backwards. Your compass is external which way is it pointing? Currently you have it set for pointing backwards as well. Remember compass orientation is relative to the autopilot orientation so if your autopilot is pointing backwards and your compass is pointing forward you need to set 180 degree orientation on BOTH.
I'll keep looking and let you know of anything else I find.