Are the brakes all OEM, except for the brake lines? The brake lines would not cause the squeel. In my experiance with all brakes, squeeling comes from a build up of brake dust and it kinda glazes on the brake pads the only way to get rid of the squeel is to go do a brake run-in. Swopping rotors and pads will clear the squeel too unless it's metal to metal type squeel then it would be more of a grinding sound from like a pad wear indicator or something.
I've had this on my 2004 Saab 93 Aero, even my OEM M3 brakes for a while, my AP's, my dads Alfa Romero in all cases it was caused from light braking over time. So then I'd go do a brake-run in (repetative 50mph to about 10mph gradual braking to harder braking) this causes the brake pad material to transfer onto the rotor disc and clear the pads of glazed brake dust.
check out StopTech's or APracing's brake run-in procedures. If you do something of the kind, I think it'll clear the noise out for a long while, plus improve braking.
This of course is if it's just brake dust build up or the pads getting glazed. Disc warping would cause severe vibration in the steering wheel and/or felt in the pedal while braking. I don't think that is what you have from what you mentioned. I think its just the pads need to be run-in with some hard braking intervals.