I have an 05 S, Just bought it about a month or two ago.

2 days ago, I noticed my clutch went soft, and when the car is running I can’t put it into any gear. If I do manager to get it into gear and start driving, the shifting feels wonky. I’m done driving the car until I fix it so I don’t damage it. I did some reasearch and checked the clutch master, and in fact mine is most definitely blown. My question is if I replace the CMC, with it also fix the shifting problem? Or do I have two problems on my hand now?

 

Soft clutch pedal and, as verified by you, a blown master cylinder are most likely your only issue here.

Replace the clutch master cylinder, top it up with fresh fluid, unbolt the slave cylinder on the transmission, turn it up-side-down so the bleeder nibble points straight upwards and crack it open, let gravity push out old fluid and trapped air, make sure to never let the master reservoir run dry, tighten the bleeder nibble.


Broken clutch master cylinder most likely introduced air into the system which likes to get stuck inside the slave cylinder.


Since you already unbolted the slave cylinder, feel free to polish its rod and clean out all the old grease, re-grease with Honda Urea grease:


Another important step for smooth shifts:


Once you are done with these, all you have to do is replace your clutch fluid with every oil change and it's pretty much bulletproof.