I've got exactly the same set up & posted a query regarding it on the MCN website & got this reply :
"Inside the fuse box, is the Motronic codeplug. This controls the setting for the fuel injection system. It is usually a little pink coloured box located in the middle row of the fusebox. Working from the nearside of the bike, middle row, the first segment of the fusebox is empty, the second segment should contain the codeplug, the next two segments contain little black boxes (ignore them).
From what I can gather, these codeplugs are colour coded for various settings. For example, it seems pink is for standard silencer and cat. No plug connected in this bit, is for standard silencer with NO CAT.
Therefore, you could try removing the plug altogether. This could help balance out the fuelling to match your Y piece and may help remove the banging. It should certainly make it fuel better.
If you do remove it, then you MUST do the following very simple procedure.
1. Remove and then replace the fuse for the Motronic system, its No: 5 I think (I am at work and don't have the book in front of me). This resets the brain back to default and removes any error settings.
2. Switch on the ignition and BEFORE starting open the throttles to full, twice. Then start the bike.
This will reset the brain for the new settings. Then give it a go.
I have discovered all of this from investigating why, when my bike and my mates came we didn't have this codeplug fitted but another friends bike did. We fitted Y pieces early on so we did not suffer any ill effects. My bike has now done 22,000 miles and goes as well as any other. It still bangs now and then, but nowhere near what your appears to be doing. "
I've done all this & it appears to work.
Good luck.
Tim