I have two suggestions...
First, you need to do a good warm-up before throwing - not stretching. The soft tissues are more resilient and immune to injury when they are warm. Stretching alone doesn't do a good job of warming up the body.
Second, you might be trying to lengthen your stride the wrong way. If you are simply reach with the front leg, that is wrong. You need to get your momentum going while maintaining a good knee lift (either high or back or a combo of both).
However, after you're done throwing is a good time to stretch and I would recommend stretching the hamstrings because after you release the ball your torso flexes forward and puts a stretch in the hammy of the stride leg.