Vibration, thumping, steering wheel issues, wheels hot, boost going up as engine "fights" brake drag, etc - been there done that on a Dodge Ram, a Plymouth minivan, and a Mercedes. You have a "grabbing" disc brake issue and the vibration is the disc grabbing essentially imperceptible run out on the rotor aggravated by slight warping as they get hot which goes away as they cool.
Common cause is associated with the use of caliper pistons that are not stainless steel but rather a synthetic and it is not uncommon for the problem to show up after a brake job that bleeds the system while retaining the old caliper assembly. The synthetic piston(s) absorb brake fluid and tend to stick in the bore so they don't allow the pad to retract off the rotor which can result in random light pulsing or in extreme cases, I know, violent wheel hop. Symptom sometimes goes away if you really stomp on the brakes coming to a complete stop and then drive off.
Other causes could be: 1. dirty brake fluid in caliper; 2. bad brake lines - the flexible sections not the hard pipe. Those sections have been know to get soft and produce strange caliper piston pressure issues. 3. problem with the master cylinder and/or power brake boost system. 4. I'll go out on a limb a bit and speculate that the 06 stability control system might could go "nuts" from time to time and do this too.
There is nothing "special" about the CRD brake system; it's the same as the gasser one. I'd suggest you get with a good local brake shop for a chat.
Your key off comment suggests the cause may be vacuum related which suggests power brake boost system as keying off would shut the vacuum pump in engine off and drop vacuum which I'm guessing would cause the brake boost system to "back off" if it's doing something it shouldn't be doing on its own so to speak. I don't know the keying off would turn off/reboot anything in the ABS system that would do this but that's also something to consider.
_________________ Sold to LOST member my 05 Ltd, GDE Stg II turbo + TCM tune, SunCoast TC w. Transgo kit, Steiger window regulators, Samcos, Fumoto valve, 2nd gen filter head with Lub. Spec. bleeder, Hayden clutch & 11 blade fan, inverted spare, P-1 battery, BF Goodrich Long Trail TAs, Etecno1 glow plugs, timing belt at 50K miles/8 yrs
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