I have worked on many of them and can tell you exactly how to fix it. First you will have to pull the door panel off. Once the door panel is off, you will need to peel back the plastic dust covering. The glass has two plastic attachments glued to the bottom of the glass. There is a 10mm bolt going thru each attatchment that holds the glass to the regulator assembly. You will also find a vertical channel that the front leading edge of the door glass runs up and down in. That vertical channel also has 10mm bolt towards the bottom front of the door.
Now the fix:
Unbolt the 2 10mm bolts holding the glass to the regulator. Then unbolt the 10mm bolt holding the front vertical channel in place. Grap the top edge of the glass and tilt the front edge of the glass down and the back side of the glass upwards. Now you should be able to reseat the glass properly into the front and rear channels. Once you have it seated into the channels, slide the glass back down and line up the two attachments at the bottom of the glass with the regulator. Then rebolt the glass to the regulator.
If the glass does not still run up and down evenly, two things could be wrong. The Honda window regulators are made of very light weight metal and get bent or tweaked very easily. If this is the case, very often you have to replace the regulator. I have had very little luck getting them bent back correctly. Impossible to eyeball it.
The second possibility could be a simple fix of adjusting the third arm on the regulator. The third arm adjust the horizontal tilt on the glass. The third arm is just a small horizontal channel that bolts to the inside of the door and one of the regulator arms attatch to it with a roller. Just unbolt the side of the channel with the slot adjustment and move the channel up or down until the glass sits in the opening properly.
Lastly. Spray some silicone lube into the rubber run channels that the edge of the glass runs up and down in.
Hope that helps. Feel free to pm or email me if you need further help.