So, I threw the frontend back together earlier this week and discovered the same clicking noise. Previously, I had assumed that it was a poor stem fitment/bearings in the headstock; it was not. After assembly, and presentation of the same click, I investigated further. What I found was this, the floating discs shift on their buttons when the brakes are applied :-/ I visited the gsxr forums and found that this is normal, as well as some noise from the cartridges. I'm out a chunk of change to rule out the noise, but it has been determined. I spent the time the frontend was apart polishing the forks even more, powdering a few pieces, swapping another tire, and rebuilding my starter clutch. Pictures to follow soon.