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If you know your clutch is good, your fluid is good, and your shift linkage is intact and you still have a shifting problem, you might have an internal transmission problem. I’ve run into two main things here: problems with bearings and problems with synchronizers. These are fairly straightforward to replace with the right tools.

 Manual Transmission change shaft diagram

You might need a bearing separator and a press to do so, however. Be sure to keep everything in order while you're working. If you can do this, you should be fine. Consult your service manual for specifics on your application.

Every once in a while, you run into broken gears inside the transmission. If you have broken gears inside your transmission, then it might be time to replace it. The gears are the most expensive parts. You might find it's cheaper to just replace the transmission instead of replacing the broken gears and everything that goes with them. As with any repair like that, weigh the cost of repair against replacement and choose the most economical path. If you haven't done internal transmission repair before, I would advise you either take it to a professional, or just replace the transmission as a unit. A failed repair would mean the added expense of replacement on top of the time and effort you've already spent removing the transmission to perform your repair. If you decide to repair the transmission yourself, know that you're likely to need a few special tools. Consult your service manual before you start digging in. This way you'll know what tools you might need for the job you're attempting before you get past the point of no return.