Nail item before each paper item (7)
CLIPPER = nail item, (paper)CLIP before PER (= each)
After shooter’s return, receive big chunk (6)
NUGGET = big chunk, GUN< (= shooter) + GET (= receive)
Encourage bone disease (4)
SPUR = encourage, = bone disease
Lost charge of gold and silver - lies! (4)
BULL = lies, BULLION (gold and silver) - ION (charge)
Theater costume’s warmth (4)
HEAT = warmth, hidden in tHEATer
These are all
Singulars of NBA team names.
In #2, the composer's name "Gerri H. Dern"
...anagrams to RED HERRING.
The notes in #2 are
F G Ab Bb C Db Eb F Eb Db C Bb Ab G F, which make up the key of F minor.
The marks above/below the notes
Look like morse code: . -. ---- .-. -.- .-
However, this translates to nothing in particular (EN#RKA, with the # being an invalid letter)...
Still not sure about #3, but I think I get the hint:
_____ depression (5)
MANIC, which is MAGIC with one letter changed
Generic reptile (6)
LIZARD -> WIZARD
Oregon player (4)
DUCK (Oregon Ducks) -> BUCK
“Gotcha!” guy (6)
This could be CAPTOR -> RAPTOR (from LeppyR64 in the comments)
LSD part (3)
Maybe SIA (singer of the band LSD)? With one change whis would be SIX, which with a bit of a stretch could refer to the (Philadelphia Seventy) Sixers?
What to do with a dirt road (4)
PAVE -> PACE -> PACERS?
??? (3)
In the comments, arbitrahj pointed out that this could refer to the spare letters from each clue after the necessary changes. So with C, A and V left over this one would be the CAV(aliers)?