I had two separate issues to deal with with this upgrade.
1. There was extra drag that I noticed when spinning the front wheel.
That was solved by adding the spacers behind the discs.
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2. I discovered that one of my (non OEM) discs was warped after all. I didn't notice it with the original Tokico calipers, but certainly did with the Nissins. I think that tolerances with the Nissins are tighter.
So, a new set of discs installed, from S3 Performance.
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I did a test ride today, and I was more that happy with the result. After bedding in the brake pads with the new discs, the brakes performed as I expected (just like on my ZX12R I had, and my ZRX1200). Definitely a huge improvement over OEM, and 1-finger stopping.
The ride also gave me a chance to check the performance after installing the stick coils. Starts well, idles nicely, and doesn't hesitate anywhere.