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For tuner I would recommend PCIII. Other than the SERT it is the most advanced of the tried and true tuners. I have a PCIII myself and am happy. I say the tried and true because I read that a few new EFI tuners have been released, but I haven't read any first hand reports about then yet.
As for pipes I couldn't tell you, I have S&S SPO's specifically because they add performance but are quiet.
I run with a SERT and T-Rex 3" True Duals from Hard Krome on my 05 Ultra. They are sweet and bring back the old harley sound. I believe the SERT is still available. But finding a dealer capable of tuning with one may be a bigger issue. The Power Commander PCIII is a good alternative albeit another device subject to failure. It you can't get the SERT and flash the ECM directly, then the PCIII add on is what I'd go with.
I agree the above posts regarding the PCIII. I have had them on several bikes, including my current RG.
The S/E high-flow air filter setup is good one. "If" you can, request one that has the "K&N" filter in it. Recently, they started using a different one that has a blue molded seal around both ends.
Given your stated selection criteria regarding pipes (Performance & Sound), you shold consider either a D&D FatCat or a ThunderHeader. Both are 2 into one pipes, but they definitely offer better performance. I have used 2 into 1's on an ElectraGlide and two RoadGlides. For me, they look great and the performance make them a no-brainier. Again, that's just one opinion. I'm sure we'll see some more.
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