Obviously, I can't provide solutions for your particular case but, in general, athletes have issues with basic barbell lifts because they have never been properly instructed or lack the patience to seek out and instruct themselves. A lot of back issues can be solved by getting technique correct with cues such as establishing good lumbar extension (not hyperextension), driving the knees outward, utilizing good hip drive coming up out of the hole, and maintaining the proper back angle with respect to the hips.
Properly executed back squats actually provide a very good stretch to many of the muscle groups involved and, very quickly, very tight athletes that come into the squat become quite mobile enough to do proper squats. The exercise will pretty much take care of itself when done properly. Here is a good primer:
http://startingstrength.com/index.php/site/article/the_squat_or#.UtM43tJDuSo
Similarly with deadlift - without proper lumbar extension and maintenance of a stable spinal column, i.e., an improperly performed lift - you get injured. Putting on a bit of mass, well, that happens when you get stronger. Appreciable mass gains usually don't take place unless you up your protein intake. But if a slight increase in mass means a strong runner capable of more efficient movements through a runner's range-of-motion and a more stable and upright posture being carried out for the duration of the run, then that seems a worthy tradeoff, especially as we age and fight the tendency to loss muscle mass.
I self-taught using mostly the books Starting Strength: Basic Barbell Training and Practical Programming for Strength Training by Mark Rippetoe, watched a lot of video, and asked a lot of questions. But mostly I patiently worked on good form before ramping the weight up on various lifts, until such a time that I was confident that I could do so and minimize the risk of injury. That said, the risk is always there when asking your body to adapt to a new stress, such as increased running volume and/or intensity, or moving weights in a fashion that stimulates adaptation.