How do I assign a different MIDI channel to a second CDJ400 using Traktor 3 ? A step by step would help.

Well, I could tell you it's in the manual...

Press and hold the Utility button and rotate the knob to find MIDI CH, press the knob once and then rotate it to change the assignment, then press the knob again. Press any other button to exit.

OK.Sorted. Thanks. Next question...

Is it possible to play deck A through a left hand channel on an external mixer, and deck B through a right hand channel on an external mixer using 1 soundcard from a laptop ? If not, how do I set up so I can actually MIX on an external mixer ?

I don't think Traktor can set that up in the audio preferences but if you pan each channel accordingly through the master, I don't see why not. Your best bet is to get a multi-channel soundcard for external mixer use.

Pulse. You have no idea how much you are helping me ! Thanks a ton ! I have one more question, then I am good to go (I hope).
How do I get my CDJ to bend pitch using the jog wheel, like they do in normal CD mode ? It doesn't speed up or slow down when I push or pull the jog wheel ? I know its a midi setting, but which one ?

Or, how would I get my CDJ to behave exactly as if I was using CD's ? The only setting being + and - 6% pitch ? Is there a TKS file out there ?

Yes - there is a TKS file, updated ones are to come... grab the package from this thread which has a MIDI map for Traktor in it.