The effect lasts only an instant
“Instantaneous” is an adjective that must be attached to “sensory effect” or it stops making any sense as part of that sentence's grammar.
The alternative, not-very-grammatical meaning wouldn't make common-sense sense, anyway: A spell doesn't need to say when an effect happens, when the point of the effect description is by default to say what happens once the spell is cast. Lacking any mention of a delay in a spell's description, the effect is describing the spell's immediate effect.
Thirdly, spells effects are responsible for indicating their duration. If prestidigitation didn't say how long each choice of effect lasted, then they'd be horribly ambiguous and possibly interpreted as being permanent. The “instantaneous” is the require description of the duration of the effect.
So three ways—one a direct reading of the sentence, the next a backup in case grammar is ignored, the third a pragmatic argument that the spell would be broken by ignoring the first two—all indicate very strongly that it is the effect itself that is instantaneous.
Implications for instrument fills
You can't get much in the way of instrument fills out of prestidigitation. At most you can get, as it says, “faint musical notes”, plural, which suggests a trill or other quick run of notes. But also note the “faint” part there: unless you've got a pin-drop-silent auditorium, the faint noises possible with prestidigitation are going to be completely drowned out by other instruments, distance to the audience, even low-level audience noise, or all three.
Prestidigitation is just no good for auditory additions to musical performances.
What about a glow?
A glow doesn't count as a colour, if you're looking at the second-last bullet point and reading “You make a color, a small mark, or a symbol appear on an object or a surface for 1 hour.” That effect option is phrased as a complete list rather than an open list, so the limits of the spell don't allow you to add a glow to an object for an hour.
You can make a glow (on something or on its own) using the first bullet option because that is phrased as general type of effect, with an open list of examples, so a glow is certainly within the realm of a harmless visual effect it can make. But that of course is only instantaneous, not an hour long.