i had the same problem on my ek civic, its 99 model and only had 66,000kms.
i gave the car to yarra honda and they quoted me $5000 for the rebuild including labor. i got worried n shit....i found a few honda speiclists in thomastown who only rebuilds honda transmission and quoted 2.5k for it.

anyways...i did not have money to repair the transmission and had to sell the car straight away..

i heard a lot of horror things about the CVT transmission , apparently this is the worst transmission honda evet introduced...your not supposed to hammer your car at the lights otherwise u will destroy it...