The chain tension adjuster seemed to have done the trick. I used the iphone app to measure the tension before installing them and saw it was way way too low. I think the belt was dropping it skipped a tooth. Today I managed to get to work without any walk or drops. Now I just need to get the SA hub adjusted properly.
And I went with CDC instead of CDX because I got the belt drivetrain super crazy cheap off of c-list a couple years ago. Its been sitting in my parts bin waiting for my to finish this build.
If it's worked out, great, but as others here mentioned, playing around with the alignment of the back wheel in the dropouts could have it walking in toward the flange to clear up the issue. Only thing I've noticed with that original system is that it's a fine line between having it sit where you want and having it walk in to the point it rubs the flange, usually picking up a whining or squeaking sound. Best to have or get threaded tension adjusters for the rear.
Also, even though Gates says to run the flange on the inside at the rear, I've known people to run the flanges however they work for the bike they have, when they get into something unorthodox and non-stock. Check the inside of the rear cog and see if the interface with the splined driver is dished one way or the other. I.e., if you flip the cog so that it is flange-out, does that position the cog teeth track further out from the hub?
You might have skipped a few posts. I posted a few back that I switched to flange out in order to get the chainline correct. The chain tensioners allowed me to both get the axle alignment fine tuned and get the correct tension in the belt.