My son owns a 2000 Discovery II, with 158,000 miles. The problem is there is a clunking noise from the rear differential, when this happens the "service engine soon" light comes on and blinks, when the noise disappears the light stops blinking. He went away to college and I'm just getting around to digging in to it. My first thought is the Diff is shot. But I was wondering if changing the fluid or any other problems. Also when I grab each rear wheel and pull back and forth I can hear that similar noise. Any Ideas, I would appreciate it Thanks. Bob

 

Well the diff being bad/making noise will not cause the check engine light to come on.

Start by checking the fluid in the diffs and transfer case, the fill/check plug the the transfer case is on the back at the 10o'clock position of the parking brake drum.
Check the flex coupler for cracks, it is on the rear prop shaft at the rear diff.
As for the flashing CEL, you need new spark plugs and wires, but do not use cheap wires, STI, Magnecor or Kingsbourne wires and cheap copper plugs.

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Do you have the truck with you now, if so, send me your number and I'll call you today with a list of stuff to look at and do.