I'm going to throw a couple of things out there, mostly so others can throw rocks at my thinking.
If this was a random sexual assault I find it hard to believe there were 2 guys involved. I say that because it seems highly unsual, although not unheard of for things to happen that way. Those kinds of predators don't seem to work in groups.
It is also unusual for criminals to be out at that time of morning. In college I lived in a pretty bad neighborhood for about a year, bodies in dumpsters, drug dealers, people selling stolen stuff out of the back of their car...but even there it was pretty quiet between about 2 AM and noon.
I am leaning toward a SA by a solo perpetrator. If we find out there were 2 people in the SUV that would cause me to shift more to a targeted attack.
People keep talking about her running speed. I think I heard her previous marathon time was about 8 min/mile and time was about 3:40. That would be race pace for a marathon. We know little about her training routine but it is common to do shorter runs at a little faster pace and longer runs a bit slower. I used to do sprint and Olympic distance triathlons. The Olympic distance took me about 3 hours. Many athletes do routine trainings at about 2/3 their race time or distance then step it up before a race. And for the shorter distance you try to get your pace a little faster. So if she was a marathoner, 2/3 of 26.2/3:40 miles would be 17.5 miles/2:30 and she might have been shooting for a 7 min/mile pace. She was abducted 4.9 miles from home so she would would have been about 35 minutes out. I think the timing fits with a 3:45 alarm and jumping up, pulling clothes and shoes on and getting out a bit early that day. What would not fit is being back for husband to go ride at 5:00. But they clearly coordinated on workouts.