Hopefully I'm not stepping out of bounds here... I had a similar feeling in my 1->2 and 2->3 shifts. I would pull out of first, down to neutral then back over and down to second (probably to the same effect as your holding the clutch for two seconds.) Turns out, by chance, i eliminated the "clipping" i was feeling by a.) Better rev matching instead of just coming off the acc. And b.) Getting up above 3000 rpm in those two gears.
I don't mean floor it, its still daily driving but i hold out longer before up shifting. I have a two month old clutch, fly wheel and the feeling was there in my other m, now this one both pre and post clutch change. But my shifting technique had changed and its almost not noticeable.
As far as the clunk, ive heard both sides of the story... Normal for an M, and.. Uh oh.. So I'm no help, sorry!
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