I am Lost at what this could be

04 Honda CRV: I just had new rotors / pads / calibers put on my rear 2 tires because I was getting a loud creaking sound whenever I reversed or stoped at a stop sign. Most notibly I would hear it after the car had sat for a few hours as it’s not happening a 100% of the time… Am I looking at joint or wheel well problems now? The loud creaking is still an issue…Thank you for your comments…

So, the noise occurs only when the brakes are applied?

The creaking may be due to a frozen sway bar link. If you stand on the rear bumper and jump up and down a bit, you should be able to cause the creaking noise. (There are both front and rear sway bar links, so check both front and rear).

While you’re doing that, have a friend lie under the rear of the car and try to locate the sway bar, which is a 3/4" diameter steel bar that runs between the rear wheels. There are two short sway bar links that bolt the sway bar in place. Those links have ball-in-socket fittings on the end that sometimes seize up and cause a creaking noise. If you can’t locate the sway bar links on your car, do a Google image search for “Honda CRV rear sway bar link.” Once you find the sway bar link, you can put your hand on the end of the link and “feel” the ball-in-socket fitting creaking.

This is what the sway bar link looks like:

Each end has a ball-in-socket fitting that can creak when it seizes up.

I just had a similar problem on my '99 CRV and it turned out to be what I described above. The fix is having the faulty sway bar link replaced.

For future reference, you’ll save tons of money by describing a symptom to a shop and asking them to diagnose and repair it rather than assuming the cause and telling them what to change.

Jesmed is right, it might well be the sway bar links or the bushings that hold the bar to the chassis. The bar turns within these rubber bushings constantly, and the holes wear large and often creak and even thunk.

It could also be the struts or strut mounts. They’re also common causes of creaks.
But this time, take it to the shop and describe the symptoms. Let the mechanic get it up on the lift and check it out.