With me, I do what I always do, listen for the bass first. I go through the whole song and list every bass note that's played. After that, I turn the notes into numbers based on the key. After I got all the bass notes down, I practice and play the bass with the CD until I'm fairly confident that I have all the correct bass notes.
Now, for getting the chords correct (or almost correct), I go through bout 3 different phases. The first phase is chord recognition. It really helps if u can recognize chord qualities and inversions by ear alone. A major chord in root position sounds different from a major chord in 1st inversion, which sounds different from a major chord in 2nd inversion, etc. If I notice any spots in the song where I hear a recognizable chord, I write it down.
The 2nd phase is using the numbers I got from the bass notes. I can pretty much narrow the chord choices down once I know the bass note. Once I find a chord that matches, I use my ear to figure out the inversion and then write it down.
The 3rd phase is simply using my ear to figure out problem chords. If neither phase 1 or 2 can help me, I use my ear to write down every note I hear being played in a particular chord. Usually, after I got a few notes written down, I can use theory to find the chord that will have all those notes in them.
As far as runs, all u can do is use your ears to figure out the notes being played. Sometimes, the notes are part of a scale, sometimes they are part of a chord. The great thing about a run is it's one note a time. The rewind button will definitely help u out here. Write down all the notes u hear and practice til u can do it perfectly.
After I'm done chording, I play through the chords I wrote out with the CD. Once i'm in the 90-100% range of matching the CD, then I'll post the chords. It's very, very, very hard at first, but gets easier after you've done a few. Here are some tips I can give to u or any wanting to chord out a song from a CD:
Tip #1: SELECTIVE HEARING - focus only on what u want to figure out at the time and try to ignore everything else
Tip#2: WRITE EVERYTHING DOWN - anything that u hear, write it down, it will help u figure out the rest
Tip #3: REWIND & FAST FOWARD - these 2 buttons will be ur best friends, use them
Tip #4: USE THEORY WHEN APPLICABLE - if ur theory game is decent, use it to help with trouble spots