I have a 00 civic with a d16y8 in it and it had the stock s40 trans in it. A few months ago it started popping out of 2nd gear when let of the throttle. I eventually got tired of the problem and the inconvenience (no more auto-xing) so i replaced it. the new trans i got also began having the same problem after about a week??!! so i went ahead and had the original rebuilt with carbon lined synchros and replaced the worn out rear motor mount with a new oem one with Poly inserts. The problem is this one is doing the same exact thing! it is still popping out of gear when you let off the throttle. I had the guy who rebuilt it take another look at it just to make sure everything in the tranny is sound and he said everything is good in it. No bent shifter forks or anything like that. I know this isnt a common issue in transmissions and for me to have had basically 3 now that pop out of gear all in the same way is very strange to me? other possible problems i need to look at? Im going to try some new shift linkage later today but thats all i can think of. Also, the motor is rock solid and not moving too much so i know its not that. Any other advice??

 

I'm not familiar with the s40 specifically, but if the shift linkage wasn't adjusted properly, it could theoretically be preventing the gear from fully engaging.

If you're to the point where you're using aftermarket linkages, you've probably already checked that...

 

im not using after market linkage. right now the stock linkage is on but im going to try another set of linkage from a friend to see if it fixes the problem?