Could I assume that each kind of part weighs 1 lb, and price it accordingly? 500gp for the mithral reeds, 375gp for darkleaf bellows, and...I dunno, 110gp for darkwood boards?
Sounds reasonable for a home game. For PFS... *shrug*
A silver balladeer gains the bardic performances listed below. These bardic performances all require the use of a silver or silver-stringed instrument, which costs twice as much as a normal masterwork instrument.
To determine the price of a darkwood item, use the original weight but add 10 gp per pound to the price of a masterwork version of that item.
So I'd guess a silver-stringed darkwood lute should cost twice the same as a normal instrument plus 10gp per pound.
I'd say no on the flute since it's only one material - though it's a bit odd that a mithral or singing steel weapon counts as alchemical silver but a mithral or singing steel instrument doesn't count as a silver instrument. I'd probably house-rule that as a GM.