Civic has shifting issues

You're having clutch problems. Open the hood and up on the firewall in front of where the driver sits will be a resevoir. Actually there will be two, one is the brake and the smaller one is the clutch. Open the lid and you will see that it is very low or dry. Add brake fluid to the resevoir and then pump the clutch pedal until it comes back to normal pressure. However, this will be a temp fix until you determine which is failing. It will be either the master where you added the fluid or the slave unit down on the tranny.

Check the brake fluid reservoir. It's mounted on the top of the master cylinder.A low fluid level can cause a soft clutch pedal. Refill the reservoir and bleed the system.
This problem can also be caused by a faulty or damaged primary or secondary seal in the master cylinder. A leaking secondary seal will be evident by external leak( look for leak between the master cylinder and the power booster on the firewall). Whereas the primary seal leak will be internal.
To correct either of these problems, replace or rebuild the master cylinder, then refill and bleed the system.
The slave cylinder if located close to the tranny but connected to the master cylinder( follow the hydraulic line from the master cylinder and you will find it).
Check for leak around it, if found, replace it and bleed the system.
You should also check the pedal ajustements if no leak is found. :)

OK, the firewall is the divider between the engine compartment and the dash or cab where you sit. The picture attached is a master cylinder but it is for the brake. However, they look a lot alike and they sit next to each other. They take the same fluid to make them work.

Let's not worry at all about what Mathiaso has said. He mixed the brake and clutch around a bit but in general his info is correct. Yet I think you definitely need a simpler set of instructions.

Looking at the picture above locate the smaller of these two reservoirs. That one will be the clutch. There is a hose coming out of the bottom that connects to a metal tube and that when followed will take you down to the transmission and connect to another item attached to the outside of the tranny.

Follow so far?

Now back to the master cylinder, please check the fluid level. You can look at the level from the outside but I suspect you will see little if any fluid. Now look around the master cylinder and tell me if you see any wet spots like it has been leaking. If not, then crawl under the dash with a flashlight and attached to the clutch pedal will be an arm the goes through the firewall to the engine. It actually connects to the master cylinder. Look for leaks here as well. What did you find? No leaks go to 2. Leaks read on.

Any leaks and this is the problem to your clutch not working and it needs to be replaced. Don't even try to rebuild it yourself. To replace it get one from a local parts place. The new one will need to be filled with fluid and bled. The part will come with instructions on the bleeding. Tell the parts man you want to see if there are instructions and get them. Should be in the box. Disconnect the metal tubing from the reservoir and remove the two nuts holding the master on the firewall. Take off the old master. When you have the new one bled put in on and tighten the nuts down. Now connect the tubing again to the new master. You are almost done but now you need to bleed the entire system. Go to 4.

2. If the master was fine and you saw no leaks you need to follow the tubing down to the other device. Check the tubing as you follow it for any leaks as well. When you get to the other end you will have found the slave cylinder that actually engages and disengages the clutch. It gets its orders from the fluid pushed down by the master cylinder. Look at it for leaks. Find any? If so go to 3 If not go to 4.

3. The slave is the culprit that is giving you problems, it needs to be replaced. Get one from the parts store and bleed it as talked about above. There should be instructions on the bleeding of the slave. Remove the old one from the engine and disconnect the line. Install the new one after bleeding and reconnect the line. Now go to 4.

4. If the master is fine and you see no leaks and the slave is fine, open the top and add DOT3 brake fluid to the reservoir until it reaches the max level. There should be a line on the side for min and max. Fill up the reservoir and leave the cap off. While you are down in this area you will see a nut that has an extension on it and a hole. This is called a bleeder and by slowly opening it up when put pressure on the pedal it will squirt out fluid but you really want to have it let out the air. Have a partner help you. Push on the pedal and crack open the bleeder. If the pedal goes to the floor close the bleeder and pull the pedal back up. Pump it several times and try to get some pressure on the pedal. Then crack it open slowly and let out any air. Before letting up on the pedal close the bleeder. We don't want to suck back in any air. Repeat until you get a strong clutch pedal. There is not height adjustment on the pedal. If it is hard to get the pedal to maintain or get pressure, make sure that all connections are tight and not leaking. Do not reuse the fluid that you catch in a pan. Throw it away with waster oil. Make sure that you don't let the reservoir get dry in the process keep it full. When done put the cover back on.

Let me know if I missed something. I am online a lot.

Good luck!

Bruce, you did a good job. But we both agree that I never said that the clutch pedal height must be ajusted. I have said that to check the pedal ajustement. The word" height" between " pedal" and "ajustement" come from you.
Have a good day, :)

Read my posting to replace the slave unit. Canadian should be able to get the slave or the unit can be acquired on line. They may have to get it shipped in. Not that hard of a job.