I'm out of ideas, need some input

A couple of weeks ago while returning to L.A. from N. Ca. along Hwy. 1, I noticed a change in the sound of my exhaust tone. I was just cruising along at about 70 MPH. there was nothing else that seemed to different at that moment. But when I stopped to look at things to see if I could spot a problem, nothing was visible, and restarted the bike the idle seemed to wander a little.
Then I noticed the acceleration while still quite good seemed to be not what it was. It's possible that could be an imaginary difference because of my anxiety.
But when I blip the throttle it doesn't respond as quick as it used to and it still seems lacking just a little power than what I have been used to.
Now, I've checked the fuel mileage and it's consistent with what I've been getting, right at 40-41 MPG. I've had the A/C off and pt my finger over the idle air port to check for a intake leak and the engine dies immediately when it's blocked.
I've done the full engine service on the bike also. Oil filter, oil, plugs, washed the air filter, even replaced the in tank fuel filter.
I've hooked the Thundermax up to the computer and checked the sensor log and the fuel maps and it all reads fine.
I ran a compression test and both front and rear cyls pump up to 150 PSI, while cranking the rear cyl. test it did seem to pump up a little slower but not much.
Yet I still feel something is not right. The bike just feels and sounds different to me.
This is a stock '09 TC96 with 40,000 miles, the only mods being SE A/C, slip on Samson mufflers and a Thundermax Autotune.
Even with everything I've done, I wonder if I could have burned a valve.
I don't have the equipment to do a leak-down test. Should this be my next test? I'll have to research how to do it and buy the tools needed.
Any Ideas as to what it might be and how to test for it would be greatly appreciated.
Like I said the bike still runs very well doesn't miss that I've noticed, seems to have a lot of power and gets as good of mileage as it has in the past.
since I came back from N. Ca. I've put around 800 miles on it and it still seems different than what it was.

That crossed my mind and I may try that if all else fails but everything the Tmax does can be read on my laptop. If everything is showing correct I suspect it is correct.

Harley manual says anything above 125 and 10% between cyls. is good.
I've done the other stuff you suggest except swapping the ECM.
What I'm thinking now is maybe I need to pull the mufflers and check out the baffles to make sure they haven't burned out. I've been running a pretty rich AFR, at least compared to the stock mix, through them for about 20K miles. If it still had catalytic converters that would have been my first thought but the '09s had the converters in the mufflers not the header like the '10 and now the '11 models.

I agree with HRK...the baffles might need to be repacked, the fiberglass in them will either burn up or get blown out the tail pipe a little at a time.

"Samson mufflers do not come with baffle wrap, they are all steel construction."
That's a direct quote from JR at Samson.