Ok, so I made headway when I was triple checking things and noticed the certificate on the replica server missing from Trusted Publishers (facepalm). Added certificate and this appears to have resolved my problem. I am guessing that WSUS was rejecting the packages because they weren't signed by a trusted publisher (yes, thank you ahead of time for the captain obvious award). I will post back with any further issues. Interesting thing is that the Id field still shows up orange...
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