Adjusting the bike

My left knee is starting to feel better after this weekend. I've been trying to figure out what could be making my knee hurt so much lately. I know my running miles have been down, but that shouldn't be causing it? So I started second guessing the bike, maybe it's not set up properly for my body. I've rode 22 miles in the last 2 days just running at a good pace around 17 to 18 mph. I don't think my leg was extending straight enough, so I've raised the seat about 3/4 inch & adjusted the handle bars as well. We will give it an try and see what happens. I think I'll take off a few more days of running just for the knees sake.