I don't know if you ever figured out what the problem was, but I will tell you my story. I have a 2003 Ford Ranger 2wd. I had a pulsating brake problem in my front disk brakes for 10 years until I finally figured out the problem. I bought the truck new and the problem started within the first 5K - 10K miles. In trying to fix the pulsation & wheel wobble, I replaced the disks 3 times each time with new bearings, seals, and pads. I bleed all 4 brakes multiple times. I checked the parking brake, rear brake, and the ABS. The ABS can be disconnected to simply check if this is the problem. I checked the lug torque, and properly bedded the pads on 2 different pad types (ceramic and semi-metallic). I also checked the front suspension and steering. NONE of this fixed the problem. And no matter how many times I was told the rotors were WARPED, or I was doing something wrong by some expert, nothing fixed the problem including replacing the rotors.
In trying to fix the issue again in 2011, I replaced only the brake pads with semi-metallic's as all the previous pads I tried were ceramic (I was still on my second new set of rotors). I decided to grease the caliper slide pins with caliper lube. The pins were well greased and slid nicely when I was done. SO, fast forward to a couple of days and the problem came back. I didn't think anything of it until I decided to replace the rotors and pads again for the third time a year later. After replacing the pads and rotor on the passenger side, I was just about done with the driver's side when by chance, I happened to check the caliper slide pins before installing the brake pads. I figured I did not need to bother with them as I had just greased them a year prior. To my surprise, the upper pin would NOT MOVE... The lower pin slid out no problem, but the upper took quite a bit of force to remove. (I think I used some pliers). In looking at the two pins, the only discernible difference was the rubber collar (or boot) that sat in a wide groove in the upper pin. I then looked at the pad and noticed that the pad was worn uneven.... It all started to come together!
According to the manual, a special lube was used on the caliper slide pins. They recommend not to remove it as there was no replacement for the grease at the time, but I think it's just a good silicone based grease. Regardless, I tried using silicone grease, and even making a new rubber collar to put in. I finally decided to just remove the STUPID RUBBER COLLAR! I was going to go down to the local Autozone and pick up a new set of slide pins and use the same solid pin without the groove for both the upper and lower. But I realized this was not necessary. The groove in the pin is well within the slide housing. The shear plane of the pin is at the largest diameter for both pins. Removing the boot will have no effect on strength or safety. In fact, I believe the boot is simply for noise and vibration abatement (isn't that ironic). BTW, for those who are going to say removing the boot is unsafe, please tell me how. I happen to be a Mechanical Engineer, so feel free to get technical.
So, I realized, my vehicle probably had very little lube from the factory, or moisture intruded into the caliper slide pin housing and caused the rubber collar to swell (or both). When you first drive the vehicle, everything is cold, but as soon as heat is pumped through the brakes, everything expands making the problem worse. The swelling causes the pin to seize on that side of the caliper causing the pad to apply uneven pressure, which in turn causes the pulsation. When I finally decided to apply some caliper slide grease the first time, this made the problem even worse as the as the rubber collar requires a grease that will not cause it to swell. It wasn't until my last go around with the pads and rotors that I discovered this and removed the rubber collar from the slide pins, one on each side. I have had not an issue since then in three years. I love driving my truck without pulsating brakes!
I can't tell you if this is the problem on your vehicle because you may not have the rubber collar. If not, then the best this will do is make you check the slide pins. But if you do have the rubber collar, I highly recommend you check this as it is very simple and inexpensive to fix. And you can check it by removing the rubber collar and trying for no cost. It just so happens that I also have an Infiniti I35. In replacing my brake pads last time around, I decided to grease the caliper slide pins on it. One of the pins on each side also had this damn rubber collar! Although I never had an issue with the brakes on the Infiniti, I canned the collar anyway. Have never had a problem with the I35 either.