Now this DIY is technically for a 99 Civic SI (EM1) so besides how to remove/install the lock cylinder, the re-pinning process should be the same.
Since there doesn't seem to be a DIY on how to re-pin (re-keying) a key cylinder on here or much of other sites, specifically the trunk lock, I decided to go ahead and make this DIY for anyone else wanting to do this. I'm a big DIY type of person, only if I can't do it then I'll let a professional do it. But this is how you learn, by doing it yourself.
Since technically this is a repost of my DIY from another forum, this is still my first DIY I wrote, so if there is any flaws, anything wrong, or not as clear, then my apologies and anyone can offer suggestions to improve it. or maybe have some pictures to contribute.
So first is a boring story; since I got the car last year my key only worked on the doors and the ignition. The key did not work on the trunk, seat release, or that trunk handle lock. So I finally decided a few weekends back to figure out how to become a locksmith (kidding) and re-key the trunk lock. Not finding much DIY online on this, I had to figure this mostly out by myself, but it's very straight forward and you really don't need a DIY, but for those who need a helping hand, this will hopefully help.
A warning first hand, you may not be as lucky as me, you need the correct pins for the key to have it to work (unless you want to be ghetto and only use a few pins and make a universal lock), so without the correct pins you will be unable to finish this project. What I ended up doing was since I had no need to use the seat release (I deactivated it) I ended up using pins out of the seat release lock on the trunk release to finish the project. I also noticed that all the locks in the car don't use the same pin layouts.
So the first step is to remove the lock from trunk lid.
There are only three things you need to do here, first is to remove the bolt, guessing off hand I think it uses a 10mm, since EVERYTHING almost uses 10mm on this car. Next is that black plastic piece that attaches the pull rod to the lock, that black plastic piece just pops off the rod, just push it one direction until it pops off (not off the lock.) Next you need to carefully take the lock out, I think it's suppose to twist a direction (locks into place) but it came right out for me.
This is the lock once you have it removed:
The next step is remove the horseshoe shaped pin off of the lock.
This guy holds everything in place and keeps the cylinder from falling out.
Next up is to remove the metal piece which has the rod connector on it. It just slides up (has a notch on it so it slides off in the notches of the cylinder.)
The next step is to remove the spring.
The ends of the springs are holding in by notches on the metal part of the cylinder, this is how it keeps in place, I used a flat edge screw driver to pull it out of the notches. Make sure you get these back in properly when you reassembly the lock. This spring makes the key cylinder spring loaded so it returns back to center.
Alright final step to get the cylinder out, you have to remove that metal cap off of the cylinder, this is where the key slides into the lock.
This part was the hardest for me, there is probably an easier way to remove it but I ended up using a flat edge screw driver and hammering it off, be careful not to destroy it, you need to reuse all parts, it has small notches inside the metal cap to hold it in place. I almost stripped them out.
Alright, we finally have the cylinder out.
Now the next step is remove the pins, just slide each of these out, also, each has a spring placed with them in a little hole, BE CAREFUL NOT TO LOOSE THESE!
Each pin has a number on them, I think the numbers go from 1 to 6. As you can see in the picture, I had one 1, one 3, three 5's, and two 6's. So if I needed another 1, or 3, or even some 2's, I was out of luck. And this was the case, For my key I needed 2's, 6's, and a bunch of 1's. I was lucky and got the others from the seat release lock... and here is the odd thing, when I was trying to re-key the seat release lock, it doesn't take the same number pins the trunk lock uses, it was different. I was unable to re-pin the seat release lock, so I left it as is since I didn't need it.
I don't have a picture for re the re-pinning part, but it's simple, and this is how I did it; one at a time.
That is, start from the first pin slot on the cylinder, and try each pin until one works, I stuck in a pin, put the lock into the assembly (just sliding it in) and then see if it would turn, if it wouldn't turn, I'd try out another pin until I got it. You can also tell this by how the pins stick out, but I didn't trust that way.
After that is done, assembly is just how you took it off, make sure you get everything on... First back on is the cap, next is the spring (MAKE SURE YOU GET IT ALL THE WAY ON BACK IN THE NOTCHES), the metal piece with the rod connector, then the horseshoe shaped pin, then you can put it back on the car, when reconnecting the rod, the rod slides into the hole on that metal piece and then the plastic piece pops unto the rod (wish I had a better way to explain that.)
So there you are, enjoy!