I used to run 2-3 miles at 7:30 or so, several times a week, and in the first week of paleo my energy and stamina crashed pretty quickly. However, these two things worked for me:
1 - If you want to stay very low carb, try HIIT sprints. I jog for about 4 min then do 6-8 cycles of sprint for 30 sec / walk for 90 sec. With a short jog to cool down, this usually adds up to about 2 miles.
2 - If you want to keep the steady state cardio, then try upping the carbs. Have a small piece of fruit (plum, half of an orange) and 1/2 a sweet potato before your run. This worked great for me. I have the other 1/2 of the sweet potato and some almonds after the run.
ALSO - I found that taking 5-10g of BCAAs about 15 min before my run helped tremendously with energy levels, in both scenarios.
After getting past the initial drop in performance, I now run much better and faster than before paleo. My energy feels like it's coming from a 'deeper' place ... and I feel like I could keep going and going. Your body will adapt.
Good luck.