is there any way to mute individual pads during pattern playback?
(like to drop out the kick for example)

I've been using the level button and knob 3 but it kills my flow...

you can turn pattern mode off while the pattern is playing so you can see the pads light up as the samples are triggered. then if you time it good just press the pad you want to mute right as it is triggered. it works pretty good like that.

There is this trick showed in this video tha uses the subsonic effect, but since you are using knob 3 I think you already know that.

http://br.youtube.com/watch?v=FuA8RgHaMVQ&feature=related

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I use the trick above but with the isolator since I have a 303 and it works perfectly.

yeah, there are a few effects with level knobs that you can use to mute - but that means the mute counts as an effect, canceling out any live effects you were using.
seems like a mute button wouldn't have been too hard to add. do any of the other SPs have one?