From my experiences, I can tell you this WILL pass!!
Gomez was the same in the beginning, he went in his box, no matter how many times we took him out - his crate was not too big, not too small, we had him measured, etc... he just sometime had to go and he just went - at one point we were taking him out 10-15 times during the day and night -
However, he was not fully housebroken til he was 5-6 months - you have a few more tough months ahead of you, but stay on top of him, it's really worth it in the long run!
Usually puppies can hold their bladder for 1 hour for every month of their lives, at 9 weeks, your puppy can hold it for maybe 2 hours, maybe!
Norfolk Terrier, born 26/12/04