First, I was just about to say I just completed reading page 1-11 of the shop manual. Regarding the front brake lever, indeed only the front brake cylinders are activated. As one and all have said, the brake pedal activates one set of front brake cylinders as well as the rear brakes. Regarding the above, I admit to doing a rectal examination with my head.
I am, however, perplexed by the insistence of adding any amount of front braking with the full rear brakes in use.
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A quick definition of center of gravity (CG), toss a bike in the air and let it spin, it will always spin around the CG. A cheaper example is to cut an outline, in stiff cardboard from the latest Twisted Throttle shipment, that looks sort of like a bike. spin it in the air and it, too, will spin around its CG. Or if you have a lot of patience and a really sharp pencil the cutout, the cutout balances at its CG.
One more thing and then onward. Assume the rider is siting directly over the CG. Draw a line from the CG to the Earth's CG (really - no joke). Put the bike on a truly level surface and the rider centered on the CG (which happens to rises according to the rider's weight or drops when standing on the pegs) and that line meets the surface at right angles.
Enough about terms and definitions.
Ride up a hill and the line from the CG to the earth's CG moves back, towards the rear wheel. Add a trunk or rear pack full of lead, and it's not that hard to have a non-stop wheelie. When the line from the CG moves to or after back wheel, life becomes very unhappy. Being reasonable, move the CG line back about 6", and the load on the front wheel has lightened slightly. Hit the front brake hard, and there's slightly less braking than on a level road until the CG moves forward. Hit the rear brakes, which have slightly more loading, because they're closer to the CG line, and the CG line moves forward, the front brakes now carry more load and become more effective.
Going down a steep grade, the CG line is closer to the front brake. They've got more load and become more effective. But that's not really a good thing. At the same time, there's less load on the back wheel. Who cares, the front brakes are designed to do more braking. Unloading the rear wheel brings it closer to losing traction. Hit the front brake hard in a turn on a steep descent, bang over a bump, what little traction the rear wheel has can let go and "a body motion remains in motion unless acted upon by an external force" (Newton's first law). In other words, the back end will try to move in the direction it was moving in when the tire lost traction (the front of the bike will drag the back end along - the external force - so the swing won't be as much as were the back end to continue on its own - very broken bike, now two unicycles). The CG moves outwards and bike control becomes ...um... interesting.
Go for the rear brake first and the CG will move back, off the front wheel. Add light front brake after going for the rear brake, keep the brakes balanced, the CG line stays more or less in the middle of the bike and control is easier. The frame's settled and doesn't dip or lift (centered CG line).
And that is why I really, really, really dislike linked brakes. Easy-peasy, eh?
The FJR has them and they're not going away, so I'll learn to cope.