I own a 2011 manual tC. When I was learning stick, I would constantly shift at 2k rpm to save gas
but it always shook the engine so I stopped doing that.

Now I typically shift at 2.5k to get good gas mileage but even then I feel like the engine is struggling.

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I usually shift between 3-5k rpm. I don't give a damn about mpg - and driving all city there isn't much fluctuation in mileage when driving boring vs fun.

How many miles are on your car and when was the last time you changed the transmission fluid? Fresh fluid can do wonders for a rough transmission.

Additionally the 1-2 shift on the MTX is always rough (as well as low rpm driving - parking lots, etc) because the factory front motor mount is super flimsy. There are no current motor mounts that are still in production so the best bet is to grab a new OEM motor mount and fill it with 60A Urethane. This will help tremendously with shift shock as it keeps the motor from flopping all around. You will pick up a little more NVH but once it breaks in (1000 miles or so) it's definitely worth it.