You said you replaced the rotors?
With new ones or secondhand? were they machined?
New bearings?
Correct bearing torque? they loosen up after being replaced in a few thousand Klm.
Cleaned and lubricated caliper slides?

I would be astounded that new discs and pads would have the shakes.

My EF has this problem but I got it working real nice with all of the above sorted out. I am due to do it again but it's not that bad except at 100kph.