I’m sure there are folks around here who can help further and the advice you’ve gotten so far is about as solid as it gets but I’ll see if I can help dig a little more. You have one side working, one side not. You’ve replaced the wiring harness and bulbs for the affected side with the same result. As this vehicle is a 2004, you have a different harness than the vast majority of owners (changes in 2005 along with CEM and REM).
Really, the best thing to troubleshoot this with is an automotive circuit tester as was mentioned. They’re cheap (<$15) so no need to overdo it, you just want a 12 volt light on a probe with a ground clip.
Since I have no idea what your particulate harness looks like, I can only suggest that you visually walk the working side harness wire bundle all the way to the REM connector so you know the routing path. Remove the bulb from the working assembly and check with your light in the socket while someone presses on the brake pedal, validating the function side as a baseline of sorts. Then do the exact same thing for the side which does not work, using the working side as your reference and backup for a logical progression through the failed circuit.
I did have a chance to look into an old copy of a 2004 EWD I have lying around and I see another page (47) where the wire color (yellow) is different from the EWD version wire color (green) posted earlier. I’m adding the screenshot but don’t get too hung up on which color it is, prove this yourself by physically walking the wire. For reference, 10/18 is left assembly, 10/17 is right with A:5 being the socket designator for each side stop light. There’s supposed to be an electrical junction point for the two sides on the way to the REM (53/667), again not on any vehicle after 2005. That junction is “before” fuse F14 electrically and I believe it’s somewhere at the very back to the left of the battery, big bundle of wires I'll. That’s one place to look closely for sure.
I don’t see a PN for the harness that you replaced posted, could you please note it so we can get a visual on what it looks like and try to imagine the routing? Where exactly did it connect?
I can’t imagine this’ll be too hard to resolve if you’ll get a cheapie tester and take a few photos (with harness PN).
Please let folks know of any progress that you make, thanks.