How far did you run Matrix?
It's just like when you first start lifting, your body will adapt after a while and you won't be so sore. I'll run 3 to 4 miles in the morning, then hit the weights in the afternoon or evening. I used to run 3 miles immediately before lifting, did that 5 days a week for 6 weeks..........was in the best shape and conditioning of my life with no change to a pretty bad diet.