To tone muscles around thigh and the stomach regular low grade exercises that target the region are best recommended. Aside classic abs exercises, straight leg lifts and side leg lifts would also be beneficial.
Hope this helps.
If your a healthy weight range, and your already eating healthy and active, it's natural for women to have some fat reserves on their legs, otherwise your bones or period can be severely or permanently affected. This is really important if your still growing.
For strength and toning, inner leg lifs, squats, lunges would be good. leg press, hamstring machiens at gym might be ok... provided that you do low weight, high reps otherwise you'll build too much muscle to be a long distance runner. So maybe just have really light weights if any at all for leg lifts, squats, lunges.
Abs: ex 1: lay down on your back and keep your legs together then raise them to a 90 degree angle then back down to the floor without touching it. I usually do this for 2-3 minutes before switching to the next exercise.
ex: 2 : bicycle kick, on your back get your elbows to touch your knees as you move them around like a bike (if that makes sense)
ex. 3 on back, legs out on a 45 degree angle, you hold it there while you do crunches.
I have a few more, but just let me know if you want any more and i'll tell you :) I don't even know if these will be any good, but I'll give you my whole ab workout routine if you like ;) I use to be a long distance runner to, but I've screwed my knee :/ So that's over.
But don't fret if you have a bit of fat on you, it's important that you do, the training you sound like your doing already sounds more then adequate.
Hope this helps :)