My 3rd gear went out. 2nd gear slams in hard most of the time. Since 3rd went out. Going from 2nd to 4th makes 4th hard to grab sometimes.
can also hear from outside the car when going from N to R it slams hard. I have a 08 5 speed.


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Sounds like you need (at the bare minimum) new synchros inside your tranny. Might be easier/cheaper to get a rebuild or junkyard tranny and swap it in (usually a good time to upgrade your clutch/flywheel at this time). I would also take a look at your motor mounts to inspect for tears.

 

It also got a new clutch/flywheel last summer. All mounts are good. Just wondering what else it could be wrong.

 

You should drain your transmission fluid and see if there is any metal shaving or pieces in the fluid. Sound like 3rd gears teeth are gone and forth possibly on its way out., and the synchros are probably damaged.
When you skipping to 4th gear from 2nd, are you revving higher (4k-5k RPMs) that you would to shift normally or shifting as you would normally when shifting to third (around 3k RPMs)? If not you, probably should be in order to engage 4th properly. You could also inspect the shift cables so see if there damaged.

Overall your issue is most likely internal, so like drizzoh said