From experience I wouldn't use the Rocket 3 m/c, I believe it may give braking a very wooden feel. I also bought a Rocket 3 m/c to use with the F3 calipers, but only if the Bonnie m/c was too sloppy. But with the Bonnie standard m/c the brakes are great, plenty of feel and plenty of power when applied in anger. Having said that I use a single line down to the bottom yoke where it splits in to two as opposed to using a double line going from the m/c to each caliper. Just my prefered setup to minimize the length of brake lines and also less fluid to compress.
Just my opinion, but, it will most probably be a nightmare trying to get your old lines to fit and look good, I would buy new custom hoses for your new setup.