I want to clarify some points for you, which will help you decide what to do:
- You've been working to add muscle and mass.
- You've only been working your legs.
- Muscle responds to Specific Adaptations to Imposed Demands (SAID principle)
What is unclear is whether you want to keep a more balanced physique with increased mass, or reduce your mass to where it was when you were 40kg. The recommendation depends on the answer to that question.
If you want to balance your distribution of muscle
The simple answer is that you need to require more from the muscles you aren't really using right now. The weight room is the most straightforward way to do that. Yoga and Pilates will build enough strength to hold the positions required for the activity. The end result is a well distributed musculature. How pronounced you want those muscles to look depends on the amount of body fat you carry. More fat hides muscle definition, less fat shows it off.
Your goal with this approach is to increase the size and proportion of your muscles so that they look good together. You'll probably have to increase your body weight some more since you've been underweight for so long. That said, training your upper body will balance out the proportion of your thighs to your arms and torso. Your calves may be genetically small, but focusing directly on them with standing calf raises will help them grow as best they can.
If you truly want to reduce the size of your thighs
For this case, I would recommend slowing your pace and working more on endurance. Fast pace running for short distances increases the type 2 muscle, which takes up more space. Endurance emphasizes type 1 muscle, which is more compact. Running long distances is fairly catabolic, so it will reduce the size of your thighs.