It's not surprising that a dealer wouldn't be able to tune your bike correctly. First, let's start with the stock TOR tune. This is for TORs with cat bypass. Do you have the cat bypass? This tune is restricted by closing the secondaries significantly in all gears at RPM between 1709 and 4349. The first thing to do is get TuneECU and a cable and open the secondaries 100%. You can rip the secondaries out and tuning with a PCIII in 4th will produce trims good for all gears. This is not an ideal option. Even when the secondaries are set to 100%, they CLOSE in idle. This could be problematic so I'd leave them in.
The TORs tune will be too lean with the triples so you can do two things: 1) Put your PCIII back in and get someone who knows what they're doing to tune it. Ask whether they're using Tuning Link or whether they tune the cells manually. Manual is better. You MUST have the PCIII O2 controller plugged into the O2 sensor connector from the ECU. It's under the right side triangle. Did D&D install it? This tuning route should cost $250-300 with a good tuner. There is absolutely no need to get a PCV or autotune. There are plenty of guys who've gotten great results with your setup with a PCIII. The PCV has a built in ignition module but you can also get one for a PCIII for the 2008 R3 (if you can find someone to tune it.)
Wayne MacDonald at Tuneboy put out a custom tune for TORs/cat bypass & triple unifilters. He did change the timing. On the other hand I met a guy at my dealer who had Jardines and triples and they got 157 hp, 150 ft lbs with a good PCIII tune. If you could bring your bike to Freedom Cycle in Reno, you'd have no PCIII tuning problems; 2) Take it to Wayne Tripp.