Ok guys, The job is done. This is what I learnt along the way, both from other posts and my own findings.
This is for a post 2009 R1 fork conversion or Ohlins FGRT 206 conversion on a naked bike.
Parts needed
FGRT 206 forks (2009 or later R1 forks)
2009 or later R1 front fender (I got a 2009 fender as the colour was a direct match for my bike, pearl white)
R1 calipers
R1 master cylinder
R1 rotors (or 5mm spacers)
New FZ1 brake lines with 65mm extension on master cylinder line (good excuse to go braided)
Rizoma fluid reservoir mount (CT451B)
Rizoma mirror adapter (BS770B)
Rizoma mirrors
Brake and Mirror setup
If you use the stock master cylinder instead of the R1 master cylinder you don't need the extended brake line or use aftermarket mirrors and mirror adaptors, but the reservoir is a different volume. The reason for the length difference is that the banjo fitting on the R1 MC is 65mm further out on the bar than the FZ1 MC. If you cut your bars down a lot you could get away with it, but not a good idea.
I was told the FZ1 lines would fit, but for me they were too short, different years may have different length cables and the S and N versions may be different. My bike is the 2010 FZ1N (Australia).
Because the R1 master cylinder doesn't have a mounting location for mirrors, and I run a naked bike, I had to buy the Rizoma mirror adaptor to mount my mirror to. If you go bar end mirrors you don't need this item. Due to the Rizoma mirror adaptor having a right hand thread and the FZ1 right hand mirror having a left hand thread I had to also by after market mirrors and mirror mounts (I chose the Rizoma 744s, mirror mounts are sold separately).
The R1 has the fluid reservoir mounted to the front of the top triple clamp which is not an option on the FZ1 (the control panel is in the way, and it's too low). To overcome this I bought the Rizoma reservoir mount and mounted it clamped between the brake housing and the Rizoma mirror adaptor. I had to use a different (longer) bolt to mount the reservoir to the mount and made sure I used loctite on all the nuts & screws.
R1 calipers are needed as the FGRT 206 has back mounting bolts instead of the FZ1 side mount bolts. Plus you get 6 pot brakes instead of 4.
R1 rotors are 310mm diameter while the FZ1 has 320mm rotors. You can either have 5mm spacers with flanges machined up to match the counter sinks in the forks and calipers, or buy the smaller rotors. I have access to a lathe so had the spacers machined up, plus I like my aftermarket rotors.
Fender
The FZ1 fender has the mounting holes 20mm lower than the latest R1 fender which the FGRT 206 are designed for, so the stock fender will rub on the tire and can't be used.
Result
This has made a huge difference to the bike's performance. Due to the front being about 12 - 15mm lower, the turn in is much livelier than before. The shocks have made the ride oh so smooth. The change of direction is effortless. I took it easy for the first few rides to gt used to the new handling of the bike, but I like it a lot

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