I was having back problems initially with the deadlift and running a couple of years ago. What got me over the hump was to designate deadlifts with one day a week for emphasis on strength and one day for endurance. The strength day was singles with 85% maximum with 20-25 seconds rest between for 7-10 reps; the endurance day was 65% max for 6 reps, rest 30 seconds, then 6 reps, rest 30 seconds, 6 more.
Make sure you're doing side planks for your obliques and quadratus muscles...it's surprising how much these muscles play into the simplest movements. One other mistake I was making was not stretching the Lats after back day. After starting that, the pain was gone in about a month. I guess you have to look at the overall picture...muscles, as they get stronger, get shorter, unless you take care of that.