First of all, let me say that I think the vacuum boost system is the first thing to check.

Also, if both rotors on the front are warped, it is possible for them to go "in synchronization" at times and at other times be perfectly out of sync. What I mean by this is the warping of one rotor causes a pulsating feeling. Well, you add a second rotor, that pulsating will either be in phase (larger overall pulse) or out of phase (they cancel). As you go around turns the "phase" changes, resulting in the pulsating being worse at some times than others.

Warping is typically caused by a frozen caliper piston on one side of the caliper assembly. This means you are applying pressure against only one brake pad, generating heat on only one side of the rotor. Uneven heat causes the warping.

This also can reduce stopping power.

There are other reasons for brake rotor warping, but I think I've mentioned the most common. You may be looking at a front end brake job with a rebuild of the calipers. An inspection with the wheels off might show one brake pad considerably more worn than the other on each side. If so, that points to a stuck caliper piston on the side where the pad isn't wearing.

Ken300D