Wow that's a lot of Vaseline! if you haven't buttoned her up yet, you might want to wipe off some of the excess, otherwise the rotating shaft will sling it all over the inside of the shell. Glad you found the source of the noise.
In looking at your photo, in your specific case the root cause is actually a mis-alignment between the motor, and the shaft coming out of the gearbox. It's not extreme and the U-joints can compensate. However- if it's possible to adjust the angle of the motor and there's room to do so, you could align them and make the problem go away altogether.
