I had the same problem. I put laundry detergent (the liquid kind) on my feet and squeezed in. Just wear them around the house and they will slowly break in.
Not to be a dick...but I had to struggle through about 10 painstaking sets before mine were right. I never thought it would happen and I almost got rid of them...now they're money.
tweak those suckers and if you REALLY want to, while your watchin some TV, slide in those things and just work em back and forth. once they get broken in, those suckers are AMAZING!
I had the exact same problem with my old black 3DS and after 1/4 season they were perfect. Then the one of the lace loops broke. Pro: got brand new 07's. Con: I'm still breaking them in.
i got the 3ds bindings last year and it took 5 sets for them to break in. they are super comfy now though. i love them. i wore them around my house for a while too. use soap to get in, that helped me