You don't exactly have all the details here, but I'll roughly guess the timeline. It sounds like you had a stress fracture at the end of the track season and you ran on it anyways. All I'm guessing your track season ended about two months ago, we'll call it 8 weeks. That should be enough time for a stress fracture to heal, especially if you spent any time on crutches at the beginning.
You say you spent some time on the elliptical yesterday and today woke up with pain around your achilles. Was the initial stress fracture pain on the front side or back side of your shin? And is the pain today on the front side or back side of the shin? Again just guessing here, but it sounds like the pain is in different place. I personally don't like the elliptical that much because my feet and lower legs move around more than they should I think, which causes a lot of soreness. If this sounds like the case, then I wouldn't worry too much about it. Elliptical really shouldn't be putting that much pressure on your stress fracture, especially one that should be so far along in healing.
If it really has been 8 weeks or about that long, eventually you need to just try running again. I forget what my coach's advice was, but I think the first day back should be 1 minute running, 1 minute walking for 10 minutes on grass. First week, slowly reduce the walking time until you are 100% running, but still only 10 or maybe 15 minutes per day. Then work your way back from there. You won't be ready at all for early season in cross country, but you want to take it slow with the stress fracture. But, I'm more inclined at this point to believe the elliptical is aggravating something other than the original injury.