I am on the Strong Lifts version of SS, and no, squatting 3x a week is no problem as long as you have a proper form and switch to an intermediate program when appropriate. I suggest that you eliminate one of the runs however, once it is starting to screw with your recovery. While the weights are light, you can mainatin the pace. It is also a recommendation to add 20 min steady-state cario after lifting in the beginning. You will be flying through light weights, and will have time for it. You can keep yourself in a 5K run shape with 1 run a week easily.