Although a carbon fork and disk brake setup is probably an upgrade to most people I would hate to have to buy a fork, caliper, disk and wheel because of brake chatter.
For what it's worth I got a 2009 cross check used which made terrible noises from the front brake. I switched out the pads with some basic jagwire ones, set them up properly and the problem went away. I know you've changed pads multiple times so no need to go through that again. If it hasn't been done yet I would pull the brake arms and coat the posts in grease, re-install them, check toe-in and retry.
Is it possible that a slightly loose headset would cause this? That hasn't been my experience but I wonder.