Mirrors and the assembly that they are attached to are very delicate. You need to be very careful when working with them. You should never touch the surface of a front silvered mirror, such as the two mirrors in your DSLR's light box.

This really is not a DIY type of repair. You're likely to just make things worse. There are a lot of delicate adjustments that must be perfectly right in order for the focusing system to work properly. The optical distance from the lens to the viewfinder via the main mirror, the AF array via the secondary mirror, and the sensor when the mirror is up must all be the same or focusing errors will occur.

In your image above there are fingerprints evident on the secondary mirror's surface. The surface with the prints is actually the reflective coating on the front of the glass. It's not like a more normal mirror where the reflective coating is on the other side of the protective glass plate. It is very difficult to clean smudges from such mirrors without damaging them and should only be done by someone who really knows what they are doing.

As it stands now, even if you get the mirror operating correctly, your AF system's performance will probably be impacted by the damage you have done to the secondary mirror. With the smudges left in place some of your AF points probably won't work at all. If you try to clean them you'll risk removing some or all of the reflective coating. With less reflective coating the light going to the AF sensor will be dimmer. With no reflective coating no light will reach the AF sensor for the spots on the mirror which have had the coating cleaned off along with the fingerprints.