The stock system is supposed to be loud (97db). For reference, most Ti-Force systems are 98db (the Ti-Force system for the 04 R1 is 102db).
You might want to think twice before changing the system. Someone has posted the results of removing the plastic shroud and it looks very good.
However, there may be a performance and safety benifit to going with a full system that smooths the power delivery. The Akra does this at $2400 - possibly the Graves - Ti-Force also. We need to see dyno results on the systems.