I don't know about the Jardines, they probably have a slight advantage because of the free flow headers. I went from D&D's (one baffle removed) to the TOR's on my standard R3 (three pipes). The sound IS much better and I really like the "stock" look of the pipes over the D&D's leaving one side of the bike naked.
I didn't lose any performance after the change, they flow just as good as the de-baffled D&D's did. Losing the Jardine header might make a very small difference, but nothing sounds as good to me as the Triumph Off Road pipes, perfect comprimise between loudness, looks and performance.
I'll bet you could even find someone here to trade with.