Well, one at the time. eh?
The EFI EVO's have a different Crank sensor then the TC's but it's still pretty much in the same place, on the left case next to the stator plug.
I think you are barking at the wrong tree. The way you describe the problem it sounds like a misfire under power. While it could be anything, odds are it is electrical (as in ignition) or a lean misfire. While the fuel filter should be changed now and then, a filter or pump problem would show the bike loosing power under full load, sort of like dragging an anchor.
To be honest with you, I don't think you have followed thru with checking the basics, intake/vacuum leaks, replacing plugs and wires (they are good at best for two years), etc. The other thing you can do is run a strong injector cleaner thru the bike, as a injector with a bad spray pattern may cause something like this.
I also disagree with your dealer. It is obvious you will not find a code if there is no engine lite, but you can scan sensor values and see if you can find a discrepancy or unusual reading.
I can just tell you one more time, and it is just a guess, but if you have eliminated all the basic things, the odds on suspect is the ETS and to a lesser degree the Cam sensor. When Crank sensors get weak, the bike is usually very hard to start or will not run at times. Odds also are a Crank or Cam sensor, and even a TPS will set a code. The ETS on the other hand can have shifted values and not set a code.
With these things, even if one is there in person, one has to work with hard data, and that means reliable measurements and numbers.
The only other thing you can do, if you have a friend with a garage, is to hook the bike up to a infrared exhaust gas analizer and get CO and HC readings, preferably when the bike is showing the symphtom. Then tell me what the readings are.