Realize this post was from last year – but I hope someone can successfully delink this brake system. It’s the only negative part of this bike, in my opinion. Currently replacing the whole secondary master cylinder – bought it when the 07 was still under warranty and knew as often as I get into rain – it was going to be an ongoing problem. 30k miles on it now and rear brakes lock up regularly just as they were designed to do. I’ll never pay money for another bike with linked brakes – it’s now the first aspect of a bike that I research when one looks interesting. Best of luck!
I have done a de-link on my VFR800, mainly so I could use some better 4-piston brake calipers on the front end. In addition to plumbing in the 3rd piston in each caliper, you do need to consider the hydraulic ratio between the master cylinder and caliper pistons; if the ratio changes, then the brake power/lever travel will change. As a guide, using more caliper pistons would need a proportionately larger master cylinder (by area).
At the back of my VFR I substituted the brake master with one off a CBR600 (you will find most Honda back brake masters use identical mounting points), and joined both standard brake hoses at the master with a double banjo bolt, which has been perfect and easy.
For the front as WJB says you would need to link up the 3rd pistons at the caliper, I know this has been done (on a rear VFR caliper) by drilling internally to connect the piston chambers and then plugging the external port with a suitable bolt/washer. After that you would need to replace the SMC with a suitable rigid connector.