Have you pulled the wheels to measure brake pad thickness? Grinding when coming to a stop can point to worn brake pads. Do this before going any further.

 

 

Does every gear do this?
Does it sound the same in every gear?
Does it make any sounds when not engine braking?
Can you actually localize where it's coming from?

 

 

Have you had the transmission out at any point? It may not have been aligned correctly when it was replaced.
How old/what condition are the engine mounts in? If one has collapsed, things could be really moving around in there. Same for diff mounts.

If not the above, since it's specifically engine braking, I would look at the diff. How old are diff and trans fluids?

Any engine noise will vary with rpm, while most trans and diff noises vary with vehicle speed. You can use this to narrow down what's making the noise.

If nothing else, get the car up on jackstands, run it and try to recreate the sound.

 

I agree with Loki that it might be a driveshaft alignment issue. If the mounts all look good then it is likely a worn universal joint on the driveshaft. If the joint has too much play then the torque load from downshifting will load up the joint bearing causing it to make noise as described.