SS, I've experienced all of the same problems when introducing speed work and did very little until this year. I now do the vast majority of my speed sessions either on a track, which has a much more forgiving surface, or on grass. Since adopting this approach I haven't had any major problems, although I still get the occasional small niggle or two.
However, having done quality speed work for nearly 4 months I have come to the conclusion that it hasn't really helped me that much. What works best for me is doing long intervals (on the track or treadmill), tempo runs at 10k speed and my long runs at near to marathon pace.
So, rather than do the "normal" speed sessions, why don't you simply try the above. It may work for you or it may not but at least the risk of injury will be minimised.