The New York Times' On the Run blog has an excellent article titled "When to Push Through the Pain is a Difficult Question."
I agree that pain can be tough to assess. However, as an experienced marathon runner with a 3:07 PB, I highly recommend you listen to all the signals your body gives you, during and after training.
While soreness in training is common, particularly near the end of long runs and speed sessions, you should feel a lot better after a shower, food and some rest.
Persistent soreness, tightness and - particularly - pain is an indication of trouble.
In that case an extra day of rest, i.e. no running, is a good idea. So is taking a hot bath with Epsom salts, followed by gentle stretching. You can use a tennis ball and a rolling pin to self-massage tight muscles. Simply try - it will be easy to notice which spots you need to work on.
Get a deep tissue massage from a registered provider or any other treatment that helps release tight muscles. (Note: don't get a massage too close to race day.)
While running can be uncomfortable, it should not be painful.
An example of what can happen if a (novice) marathon runner chooses to ignore persistent signs of tiredness and niggles can be found in Chapter 10 of my book Powered From Within: Stories About Running & Triathlon.
Training for a marathon means challenging our body, and often injury and illness are part and parcel of that. However, catch any issues early so that they don't become chronic and stop you from doing what you love for weeks, months or longer. It's better to be safe than sorry, for sure.