Andrew, on my 07 I did have to modify the bulb holder as the HID bulb wasn't a direct fit with my kit. Also, if you want to see where & how I housed my ballast there is a pic in this link (post #27): http://1000rr.co.uk/general-1000rr-discussion/3856-4.htm
Send me your email address and I will send you a 6 MB File incl. Pictures and Infos I collected about installing etc.
Sorry mate I meant to type search for "intake flapper mod"...(not "flapped") You can also free some space by replacing the battery with a Li-ion one. FAQ for 2008+ Honda CBR1000RR Ballast search