At the Daystrom facility Riker correctly identifies the violin notes, indicating perfect pitch. Then, in the correct key, he completes the tune by whistling the last part of Pop Goes The Weasel. He is repeating what he did during Encounter at Farpoint (1987), but with a change. In the original he whistled a half-step above the key that Data was whistling, which indicates a lack of perfect pitch.
The USS Voyager was made into a museum on the Presidio in San Francisco after it returned from the Delta Quadrant in Endgame (2001). While it is unlikely, there is no reason it couldn't have been moved.
When Alton Soong mentions the golem, he mispronounces it as "gollum".