Sounds like you have warped rotors. If you can run a dial indicator on the rotors and check the runout. If it's more than 0.008" or so, pull the rotors off and make sure everything is nice and clean and that the rotors are sitting nicely. If the problem persists, get the rotors turned.
88 LX Hatchback (100K Miles), Stock Engine, B&M Shifter, SFC, ST Brace, G-Load Brace, Eibach Pro Kit, Tokico Illumina Adj, MM LCA, FRPP UCA, FRPP FCA, Mac EL Headers, Dynomax Super Turbos, Mark VII front disc, TC rear disc, ROH ZR6 16x8, Fuzion ZRi 225/50R16, Corbeau Forza DS