1999 Ford Expedition shakes when I stop.

Sounds like its misfiring/running rough:

Could be caused by worn or fouled spark plugs, a weak spark (weak coil, bad spark plug wire), loss of compression, vacuum leaks, anything that causes an unusually lean fuel mixture (lean misfire), an EGR valve that is stuck open, dirty fuel injectors, low fuel pressure, or even bad fuel

If this is occurring mostly when you step on the brake the rotors may be warped and probably just need to be turned.