The left motor has been replaced, and motor/propellors are spinning in the correct direction. We have re-calibrated the gyro, accel, compass. We have also gone back to the previous stable version (1.4) just to see if that would fix the problem we are running into. When we manually drive it, there are no issues with acceleration or turning and it steers like it is supposed to.
I took a look at your video and log files. It definitely looks like your BlueBoat is struggling to navigate! Generally if things work as expected in manual mode, but Acro/Loiter/Auto mode struggles, you have a calibration or configuration issue.
In your case, it doesn’t seem like you’re running the default BlueBoat parameters - can you try loading them from the vehicle setup page, with the system connected to WiFi with internet?
You may need to then switch the ESC connections on the Navigator, or even reverse the direction of one or both motors - it seems they may be reversed, which would explain the oscillations you’re seeing. It is possible to setup the vehicle to drive ok when manually controlled with things reversed - this obviously causes issues in modes where the autopilot takes over control! A good test is to put the vehicle on the ground, arm and set to Acro mode, and then nudge the nose over to one side. The propellers should move air so that if the BlueBoat was in the water, it would return to the original heading. So, if you nudge the nose to the right, the left prop should push air to the front of the vehicle, and the right prop to the back of the vehicle.
Let us know if you’re unable to get things resolved! And take heart, I struggled with this exact issue when I first setup and used a BlueBoat as well!