Greetings and welcome to Just Answer. My name is Mark.

The fact that you had your brake rotors refinished, shouldn't cause you to eliminate this area. Reading your post, you state this vibration is "with" braking. Therefore the only culprit is your brake area.

You do not state make and model, therefore I have no way of knowing whether you have 4-wheel disc or disc/drum combo.

The correct way to diagnose this is to first make sure all 4 of your brake calipers, (if you have 4-wheel disc) are free, and the caliper pistons do indeed move freely in and out. Next would be to make sure all 4 of you caliper slides move freely and there are no parts "hanging" up.

Next with the wheels off, would be to actually measure the brake rotor thickness and lateral run-out. You will secure a dial mic to a stationary part, and then secure you mic to the surface of the brake rotor. Turning the rotor by hand, you can measure the lateral runout.

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There are specs for lateral runout and it is very minute. Any kind of lateral runout or thickness variation can give you brake "vibration" and/or "pulsation". Especially after the brakes are warmed up. As a general rule of thumb, vibration or pulsation coming to a stop, is usually coming from the front. Stepping on the brakes at highway speeds and feeling a vibration, usually is coming from the rear brakes.

Brake rotors now-a-days are very cheap. You can get quality brake rotors at AutoZone for less than the brake pads themselves. Also, brake rotors can usually only be refinished once or twice, depending on the amount of material removed. When the brake rotors are too thin for refinishing, they should be replaced. Brake rotors that are too thin for service will warp easily and not dissipate the heat as they should causing other brake issues.

Okay, ... you should have drums in the back. In 2000, they were notorious for leaking wheel cylinders. You should remove your rear brakes and make sure your wheel cylinders aren't leaking and you have brake fluid on those rear shoes.

Again, read the above post and with speed, it is usually the rear. You might have some warped or bent drums. Otherwise, make your measurements as suggested.