so you have an EP chassis that is currently an automatic d17, and you want to convert to a manual transmission?
First step would be to decide if you are okay with a check engine light, or if you can deal with the hassle of leaving the car at a honda dealership to deal with programming the immobilizer once you install the manual ecu.
Other than that, you will need to figure out the steps to trick the car into thinking you are in park or neutral, as the car will not start until it is satisfied.
On older civics, merely bridging the correct wires at the shifter connector worked.
No idea on 7th gen.
You also need to see if you have a factory provided location to mount the clutch master too. Again, older civics simply had a plug where it was on auto cars. Again, no idea on 7th gen