Sheraz, 6-Speed Manual ? Are You Sure It’s Not Grinding When Shifted Into 3rd Or Hard To Shift Into 3rd Or Popping Out Of 3rd (. . . Wink, Wink)?
Looks like transmisssions (automatic and manual) are not the Honda strong suit. Some 04-07 TLs have these symptoms because of faulty 3rd gear sychronizer or 3-4 shift sleeves.
The fix is to replace the 3rd gear set and Honda District Parts and Service Managers or your Zone Office consider whether you are eligible for “goodwill” after your warranty has expired.
Another problem with transmissions in some 04 TLs also considered for goodwill after out of warranty has to do with 5th gear “vibration or drone.” A subframe dynamic damper kit is installed on vehicles in which a vibration is felt or drone is heard in 5th at about 1500rpm, between 50 and 60 mph. It can be more noticeable on an incline or while accelerating.
CSA