I had similar problem, took my car to dealer and they diagnose it as excessive clutch plates wear on 2nd gear, therefore transmission needs to be rebuild. they quoted $5600 to replace it, but extended warranty did not wanted to pay that much, I went to AAMCO. total charge was $2300 but I cost me only $100 of deductible. it took almost 3week to rebuild it, it took that much time because poor communication between extended warranty company and AAMCO.
i know few guys at
www.v6performance.net who had to replace tranny but had no extended warranty, so they bitched to Honda about it and Honda agree to pay for parts, parts is major chunk of money in rebuilding tranny. main reason they were able to get Honda to pay for parts because Honda having problem with transmissions on V6 power cars (accord V6, TL, CL), they even extended factory warranty to 100,000ml for 2000 & 2001 model. there is no difference between 1998 and 2001 transmissions so you got point argue.