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My brother has a honda civic type R that he bought 2nd hand a few months ago. Every time he tries to shift into 3rd gear, there is a faint grinding niose coming from the engine. Sometimes before pushing it from neutral to 3rd, it won't engage and the stick wobbles. It will do this on 2 or 3 attempts and then engage.

What could be the problem? How do we fix it?

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    Check the seals around the master and slave cylinders for corrosion. I had a similar problem on my used S2000 that was fixed by replacing the seals (well, replacing the whole thing, but the seals were the problem). For me it started out with just 3rd, then quickly spread to all the gears until I couldn't put it in gear initially without stopping the engine entirely and putting it in gear with it off. Then I had to revmatch and force it in to get any gear but first.
    – Sam Whited
    Oct 9 '13 at 20:19
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    @SamWhited might want to specify clutch master and slave cylinders. Also, could be worn synchros on 3rd gear.
    – mac
    Oct 9 '13 at 20:40
  • @mac Hah, oops. Yup, that would be important. Thanks.
    – Sam Whited
    Oct 9 '13 at 20:45
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I'm not sure what year Civic your brother has, but I found some info on civinfo straight from Honda about this issue.

Source: http://www.civinfo.com/forum/bugs-faults-irritations/52857-honda-hints-tip-issue-no-9-a.html

Quote from PDF file (since you have to sign up to view the PDF)

3rd gear difficult to select, jumps out of gear or crunching when changing up from 2nd gear on 2007 model Type R only
Fix: Please replace the third/fourth synchro hub using the following information on your warranty claim

Casual part number: 23623PNS316
Sympton code: 0301
LON: 2131D0
FRT: 5.9 Hours
Replacement part number: 23623PNS326

Another solution besides replacing that synchro...

When I was researching these cars (considered buying one at one point), I read about third gear grinding issues. The solution a lot of the time is to switch to GM transmission fluid, as seen here on an EM2

http://www.civicforums.com/forums/36-mechanical-problems-vehicle-issues-fix-forum/324484-3rd-gear-grind-got-you-down-i-got-your-fix.html

Here's another instance http://honda-tech.com/showthread.php?t=3020743

It seems like a pretty common solution to use GM synchromesh. I found a few threads where it cured their issue on various Hondas.

Hope this helps

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