i had this problem initially, in the first month or so of ownership, even after getting inserts/SS/bushings. i come from linkage actuated transmissions (old honda) and also new style cable actuated, but one afflicted with a poor design (NEW honda Si which just came out with their TSB for their issues), so really i figured i should not have an issue with the ms3.
it then hit me that i was simply not paying attention to the clutch engagement vs. the gear change from 2nd to 3rd. it's weird on this car, trust me. it takes some realization and adjustment, but, since the middle of february, i've had no issues whatsoever, and i shift pretty quickly from 2 to 3. there wasn't any slowing down or care re: rev level, it was simply making sure the clutch was depressed before i changed gears. pretty basic idea, i know, but like i said- this car has a weird cooperation between the two. while i think the bits i bought, esp the inserts, help things, really it's just a matter of timing adjustment IMO.
now it's PERFECT, i have not one complaint!
if i had to suggest how to practice, just practice shifting, meaning taking it out of 2nd enroute to the next gear, RIGHT after full depression of the pedal. do it slowly, but briskly (if that makes sense) and then eventually speed up that syncronization. i know this seems dumb, and it's hard to explain, but it worked for me- it really was a timing issue for my car.