The third sentence makes it sound like maybe you only ran a single time last year.

The first two are fine, the third is a little odd. Last year I ran every day, but I have given up.

Those are three good sentences. The only criticism I can offer is that "last year" and "used to" are repetitious. Each expression establishes a time frame, so you don't need to use both of them. For that reason, #2 and #3 are better. #2 and #3 are perfect. I disagree that "last year I ran" sounds like I ran only once. It _could_ mean that, as in "last year I ran on July 4" but when you follow it with "but I don't anymore", it will definitely not be interpreted that way.