I think it more efficient to do the run first as well. However, tradition normally has the crunches and pullups first.
When I took my "getting back in" PFT, I ran it with the squadron run for lunch bunch (fat bodies). We did the run first because it was 40 and raining, and went to the gym for the rest. Even after running a 19:00 3 mile, I didn't notice any difference in my performance on the rest.
Really, 3 miles shouldn't be enough to totally sap the strength. I don't even hit my comfort zone (anaerobic to aerobic changeover) until about 3.5. People are always surprised to find that 6 miles is easier to run than 3, and I have coached MANY Marines through the myth that 3 is a lot.
Whatever order the events are in, it is very important to warm up. Take a brisk jog out to the 1/2 mile mark and back at minimum. Our bodies recover faster than we tend to think. I just ran the Cherry Point Half Marathon at a 6:45 mile pace. I ran a 2 mile warmup before the race and felt great coming off the gun. The warmup disperses the race tension that can last a whole mile for me, making the rest of the run more efficient.