The front brake rotors can warp and cause a vibration when braking. The rotors will need to be machined or in cases where they are worn to thin, replaced to correct this issue.
Problems for specific Honda Prelude years:
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Most reported 1996 Honda Prelude problems
On some models the manual transmission fifth gear can grind on upshift due to a misaligned fifth shift fork. The transmission will have to be removed and disassembled and the fifth gear, the fifth sleeve set and the fifth gear shift fork will have to be replaced to repair this issue.
On certain models moisture can get into the rear wheel bearing and cause a noise. Replacing the rear bearing and hub will repair this problem.