I've been running for about a year and a half. The only thing different is I went on two long hikes in a two week period that included walking up and down 1000+ large steps each time. But again the next day after doing these I felt fine with zero pain. The people I went with had leg issues the next day. I felt great and ran as I normally would have without issue. Then a week later the knee issues started. 

 This guy on YouTube is famous for curing knee pain through Tibialis exercises. You do Tibialis raises and it will strengthen those muscles and prevent knee pain: https://www.youtube.com/watch?v=miqsg9DGPX0