I got a 2013 civic SI coupe and for a while... I thought it was the smoothest manual transmission I have ever driven. Maybe about a couple of months ago, I started hearing the change of gears every time I shifted. It use to be fairly quite but now it seems it is getting louder and louder to the point that even with the radio on, I can hear the sound every time I shift (usually happens in the lower gears. 1,2,3)

That is not the biggest issue though. The shifting from 1 to 2 has some major jerking. The moment that I release the clutch and step on the gas, no matter how subtle I try to be in the transition, it feels as though some one rear ended me. In addition, every time I drive in second gear (and it only happens in second and first gear) and then take my foot off the gas the same level of jerking occurs...maybe even a bit more.

This is not how it use to drive. Has anybody experienced this or has any suggestions as to what it could be? Any information is helpful!

 

The jerking is powertrain related, a broken engine mount can be suspect here. But given that you only complain about a single gear jerking to such a high magnitude, the problem is most likely a transmission issue.

Powertrain shock due to excessive loads is the primary cause of these problems, and one of the biggest reasons why I service many of these units so early (usually 60,000 miles or less). shaft preload failure and synchronizer wear are most likely to blame for your issue.

In short, you need to pull it apart and inspect/rebuild it based on your complaint.