Yes, $3k seems very high for the work involved. But as you're finding
out, what you're paying for is the logistics of coordinating the
electrical work (including the rough-in wiring, which you didn't
include in your breakdown), the cabinet install, and the trim work. The
builder also knows that there's a risk of delay, callbacks, damaged
cabinets, holes in the wrong place, etc., so a portion of that cost is
padding for contingencies.
As for retrofitting, if the trim is just nailed up, it won't be too bad
to remove and replace. If glue is involved, you'll probably break some
trim, which will mean special ordering replacements for the cabinet
manf. Nothing is simple. Oh yeah, and you still need the rough-in
Personally, I'd skip the in-cab lights and focus on good under-cab
lighting, for which I prefer fluorescent.