My 80" Evo carb 10.5:1 does the same. The octane doesn't help. Even Cam 2. I'm convinced it's the heads on mine. Yours were just done. Could they be suspect? Hoist! 
Hoist brings up a point worth considering. It is possible that combustion chamber modifications may have increased the octane requirements of the engine to a point which pump gas can no longer meet. If this is the case, switching ECM’s and/or pulling the spark timing back may not be the complete answer.
There may be some value in looking at the experience of others running stock or H-D’s HTCC heads in a build with the TMAT auto tune. I suggest this because the HTCC heads seem capable if handling more relative timing and higher CR’s without issue. I ran H-D’s CNC ported heads with their domed piston in my 2002, 103 without issue in 2005. I currently run the 103+ heads with their domed 10.5:1, 113” pistons in weather that you wouldn’t put your dog outside in; including record breaking Las Vegas and Death Valley heat in 7-2005 (103) and last year’s killer California heat (115 shaded) in July (113”) with no engine knock issues.
I run a set of Branch Flowmetrics heads on my ’97 Buell S1. Branch’s kit uses a J&E, 10.5:1 domed piston with their modified “bathtub” chamber. This engine is a 100+ octane engine; you can only nurse it on 91 octane without knocking; a real PITA. Buell’s White Lightning with a Race Kit makes the same power running a 10.2:1 CR and 91 octane gasoline. Apparently the fastest burn doesn’t necessarily always ring the bell.
One thing common to the Branch equipped machines, including a ’93 modified Bagger that I used to run, they seem to have a propensity for quickly blackening a fresh oil change. I attributed this to high pressure blow-by resulting from the fast burn of the Branch combustion chamber. I swapped the piston rings out for Total Seal gapless rings on both the Buell and ’93 Bagger with no change in the oil contamination. The oil in the Branch equipped machines would appear visibly blackened after just a few hundred miles; a cammed and carbureted EVO or Twin Cam with stock or HTCC heads will run 1,000 + miles on a fresh change before the oil begins to darken.
A couple of questions that I would be asking are:
Does the engine oil prematurely darken relative to a stock or mildly modified machine?
Are the folks like Rhino who seem to be having better results with the TMAT & Auto Tune running a different cylinder head and piston package? Is there a pattern?
Take a look at a couple of “canned” SERT timing tables for a build similar to yours. Are there significant differences in the timing tables at the same load and RPM that you experience issues? If the tables don’t directly compare, is it something that can be translated with reasonable accuracy?
Beyond that, I got nuthin’. Good luck and I hope you get things working ok for the big road trip to the great north west.
djkak