There are different kinds of pain. Some pain is productive and is a sign that muscle exhaustion has been reached, and it's now recovering. Kind of like the pain you feel the day after an intense workout. If you're feeling intense pain during your workout or not long after, you might be going too hard. The hamstrings are sensitive muscles to injury and take longer to recover. Intense workouts, especially strength training, is technically injury because it tears muscle fibres so that they heal stronger. I can really only strength train my hamstrings once a week because it takes that whole time to recover again. Good job putting the strength training on the last day so that you're not running while it's recovering.
I can't be too sure, but I suspect that doing an intense run and *then* doing strength training, in the same workout, is too much. Prior to most strength training, 10-15 minutes of light cardio is all you need to get the circulation flowing before hitting the weights. It sounds like you are combining intense aerobic and anaerboic exercise, in the same day, which is hard on the muscles.
I would suggest restructuring your routine to allow for cardio or strength training, but not both, even if only temporarily. Larger muscles like the hamstrings need more recovery time especially because they are major stabilizers in the legs that are involved in all other kinds of leg workouts. If you don't heed the pain warnings and keep pushing it, your short-term inflammation can turn to chronic strain which takes a lot longer to go away.
Also... you may want to consider rolling out your muscles with a foam noodle after each intense workout.