Your achy knees while running may be due to weak hips. Strengthen the hips and running may be enjoyable again. not to mention, these exercises help shrink your hips! - I personally am not a runner, but I do happen to have very achy knees!
Doing more crunches is not always the right answer. What kind of tummy do you have: pooch, tire, stress tummy? See which of the five you might have along with helpful hints to stop bad habits and flatten your belly!