COPs and TTS supercharger project

I have recently picked up a 2005 Roadster which has seen better days cosmetically but it has a Stage 2 TTS Supercharger kit fitted which is the main reason I decided to snap it up (obviously .) I have decided to rebuild it and future-proof it a little in the process.
Part of this restomod will involve replacing the ageing coils with modern COPs from the Yam R1. I have done this a couple of times in the past with great results but never on a bike with the TTS kit fitted.
My main concern is that I have enough clearance for the crossover pipe from the plenum and over the top of the engine. Does anyone have experience in this area?
I am keen to get this one finished over the winter - it has been allegedly dyno'd at over 350bhp at the wheel!