OK, I have not read this whole thread. I followed along at the begininng however. Seems like most of the usual culprits have been suggested. I will add one more.
I have a buddy who built a custom 6.5SS. I have two of the same, built by the same gunsmith with the same reamer. I have also loaded for other 6.5SS by the same gunsmith who used the same reamer. Now my buddy had a 22" Proof Sendero on his, amd my two are Bartlein 25.5" & Proof 26" respectively.
He had tried about every powder we suggested. H1000, H4831, RL23, RL26, N565, Retumbo....nothing would get him speeds within 250fps of any other 6.5SS I have heard of without pressure signs. Accuracy was decent, but not spectacular either.
He contacted the smith, he contacted Rich, we talked weekly about it, he sent me fired and FL sized brass to measure against both mine (they were identical in every way), I FL sized them in my dies, I ran them through my expanding mandrel, We tried everything. To no avail.
Well, he got so frustrated with it, he took it back to the smith at least 3 times. Finally, after a few hundred rounds of chasing the issue, another bore scoping was done, and they thought they just might see a spot in the bore that looked a bit different. The barrel was pulled and sent back to Proof. Low and behold, he had a bad barrel. A swell was halfway down the bore, which was causing issues. He got that one in 10k barrel. Proof is sending out a new barrel, ad I am waiting to hear if they are doing anything else to help out.
So, you very well could have a barrel issue going on.