Perhaps you could give the user more space to work with, and then encourage them to fill in the form the way you want them to.
Consider the following:
1 shows that having a short line will encourage smaller writing, even if you have a lot of white space to work with. But lengthening the line in 2 doesn't change anything, since the leading wasn't increased with the line width. With 3, there's more space. Doesn't guarantee that people will fill it, but they're more likely to fill the space.
4 shows what happens when you turn the input into boxes. You more or less eliminate ligatures, and you encourage a certain size text. Unless people troll you with doing something like 5, they'll likely work with the space you give. So in 6, bigger boxes equal bigger numbers, and in 7, narrower boxes equal narrower numbers.
I also think that the size of the text leading up to the input area, though not as important, can send a subtle message regarding how big you want the user to make his or her writing.
So, while my handwriting isn't great, you see that 6 is a lot more readable than 1 or 2. Even 4 is better because it subconsciously makes me think of each number as a separate thing rather than a 4-digit phrase.