bleeding breaks on 2000 w/ABS

I am planning on replacing pads, rotors (at least the front) and the calipers on my 2000 Accord EX. Since I am doing all this work (especially replacing calipers) I’d like to flush the whole break system including the ABS. I just bled the clutch and even after I put 2 – 12oz. containers of break fluid through it, it’s still black in the “catch” reservoir i.e. a glass jar from pickles.:naughty: Break fluid in the master cylinder reservoir looks identical (filthy) to the one from the clutch MC, so I assume it was never changed all seven years. Should I flush the whole break system prior to installing new calipers or do it while I install them? From my previous “non ABS” life, I remember just removing front and back calipers, putting some kind of a catch for the break fluid under each wheel and just letting fluid bleed out while adding fresh fluid to the reservoir. I assume it’s not the best way to flush the system because there is no pressure applied and whatever gunk is accumulated on the walls of the break lines is going to stay there and continue to cause slow damage. Plus I have no idea how the ABS going to react to this kind of treatment. Can someone who has done this before on a similar Accord walk me through the procedure or point me in the right direction?
Thanks,