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Hello randolphp, perhaps some adjustment may be required of the throttle/shift cables.

With regards to shift noises, the "flush" ear muffs can a times with escaping water flow turn the prop slowly in a clock-wise turn. When you shifted the drive to reverse the prop may have been rotating slowing in the opposite direction which would initiate a "gear grinding" sound.

The "thud" sound you experienced when placing the drive in forward is typical when the outboard is not submerged in water. With the prop submerged, water will act as a dampener absorbing sound and reducing prop turn when motor is in neutral or idle. As mentioned, prevent over-revving the outboard when flushing on the trailer...very bad for the water pump (impeller).

If your considering future motor flushing's with drive shifts then perhaps an outboard flush bag may be an interesting option. There quite handy after a water pump repair.

Hope all gets worked out for you...
Best,
Angel M.