Setting gain levels for S4 and Traktor Pro 2

Hi everyone, I'm a newbie to the community s so sorry if I am posting in the wrong place.

I have a few questions about how I should set up my levels with my Traktor S4 and Traktor Pro 2 software. If it helps I'm running a Macbook retina display with an i7, SSD, 16GB RAM.

Here is how I have everything set up now:
Traktor Pro 2.6 (although nothing regarding this has changed since 2.5)
Autogain: off
Enable Limiter: on
Headroom: -6db
Channel gains (in default): -3.9db
Main out (in TP2 software): -6db
Main level (S4 knob): 12 o'clock

My mixing style consists of mashing up a lot of tunes live, which means I have to be very conscious of my levels to be sure not to clip. Now the reason I have the channel gains (knobs on S4) set to -3.9db is because I have found after testing that my loudest song (one mastered to be loudest at 0db) will never clip the channel level indicators on the S4 (turn the channel levels red). I then have the limiter on just in case clipping does happen (I would rather have the sound compressed rather than send a clipped signal). I also have my main out set to -6db (no particular reason why, never gave me any trouble). I have gone with this method for awhile, but have always noticed my mixes have had a slightly more compressed sound and come out quieter when recording straight from TP2 (with recording level at 0db). This has led me to have to turn the output of my S4 up when playing live at clubs and for me to have to increase a majority of the levels in my mix post-production.

Here is an example:
http://soundcloud.com/koalafy/futureproof-mix
-The mix was recorded with the settings noted above.
-At around 1:40 was the loudest point in my mix before post-production. There were 3 tracks playing. You can hear a compression on the sound, which is weird because when recording I was very careful to make sure I never went into the red on any channel out, the master out and the record out. According to Logic the recorded wav file never clipped, but peaked at 0db here.
-In contrast, the double drop at 31:30 was maxing out at about -5db after recording live, so I had to make it louder in post production. The same is with the drop at 54:05, had to add some db in post production. I found that when I turned either of the two tracks' channel gains up to attempt to push the master level up to -1-0db, I would clip on both channels no matter what (clip both channels but not the main level).

So here are my questions:
1. What is the best way to effectively play mashups (min 2 max 3 songs at a time) live without clipping levels, compressing the output signal or having to manually tweak the gain of every song (with the hands on mixing I do live, I just don't have time)?
2. Does the limiter in Traktors settings apply to the master out or the channel out? Will my headroom affect any channel above -6db? Or just the master when it is over -6db? I have tried taking off the limiter, but it seems like every song (even with the channel gain set to -3db) will clip the channel faders on the S4.
3. Will the level I have my main out set to affect the limiter at all?
4. Why does a song that I analyze in Logic as peaking at 0db cause the Traktor S4 channel db meter to turn red (clip?) when the channel gain is set to -3db (even when the limiter is off)? Is the db meter on the S4's channels even accurate? I assume it turning red means I'm clipping the channel out?
5. Ultimately, what should I have my channel gains, main out, limiter (on or off) and headroom set to in order to prevent any clipping, send a signal around 0db and ?

I understand if I'm asking for an impossible solution just let me know what the most efficient solution is. If it comes to me manually having to tweak levels either live of while prepping a set that's fine, but I would rather not, which is why I'm asking you guys. I've read through the TP2 and S4 manuals and they don't go into enough detail. It feels like there are so many variables to set I don't know how to arrange everything in the best possible way.

Yes, I'm using all 320 mp3s or wav/aiff
Yes, all my EQs were at 12 o'clock for testing

Any help or insight would be very much appreciated. I'm a perfectionist when it comes to my sound, and this is driving me crazy!

Thank you all!

tl;dr: I play with 4 decks live. How should I set my channel and master gains, limiter and headroom to avoid clipping but maintain a constant output level?