I had a similar experience with my 98 Civic. I took it on
a road trip, over 10000kms from Winnipeg to Los Angeles,
through Death Valley, Vegas, Hoover Dam. All in late August
during a heat wave (it was over 120F in Death Valley). My
car had 162000 when I left, which is 2000km over my Honda
Plus warranty of 7yrs, 160000km.
Well when I got back, my trannie was humming. Sure enough,
it was the input shaft bearing, which isn't the biggest
deal for DIY, but I took it in to my dealer anyways. They
offered to do the job on warranty. My clutch needed doing
too, the release bearing had been gradually getting louder
over the past 6 months, and they said they would do the
clutch while they were inside the trannie.
The only part they made me pay for was the clutch plate,
which is totally understandable, since it is definitely
a wear item. They didn't make me pay for any other
components, all others were covered under the warranty.
Oh ya, and while they were in the trannie, they replaced
all the bearings, 2nd and 3rd gear, and about $1500 of other
parts.
Total Bill: $2800 (at their shop rate)
Total Labour: $800
All in all, a great experience, i will definitely be a
Honda guy for a good long time.