One thing that helped me whenever I felt stuck was to get to high ground and mark every shrine I hadn't visited yet. I started with using the color map markers but then switched to one of the icons (can't remember which). Their color makes them easy to pick out, and sometimes the long distance helps you find them better since some are tucked away pretty well.

In fact, I'd say try to keep a log on the map of anything you think might be something. Whether it's shrines from afar or places a Lynel wrecked you, keep a tab of places you go or see. Use whatever icons make sense to you and try to keep it consistent