I got the clou!
I prepared my set's in Acid Pro, then set up Traktor to exactly what the set is. I have done several sets, each between 11 and 30 Minutes. Now everything sounds great and easy to play cos Traktor is set up for each song.
I think this is what the big DJ's do too!
I can remember in the past DJ's marked their vinyl's with tape to know where to start in.
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