Variable names:
You can write code to match variable names in one file with the variable names in the other, then you can replace both sets with a consistent variable name.
File 1: var1 += this(var1 - 1);
File 2: sum += this(sum - 1);
After you read File 1, you look for what variable name File 2 is using in the place of sum, then make the variable names the same across both files.
*Note, if variables are used in similar ways you may get incorrect substitutions. This is most likely when variables are being declared. To help mitigate this, you can start searching for variable names at the bottom of the file and work up.
Short hands:
Force {} and () braces into each if/else/for/while/etc...
rewrite operations like "i+=..." as "i=i+..."
Functions:
In cases where function order doesn't matter, you can make sure functions are equivalent and then ignore them.
Operator precedence:
"3 + (2 * 4)" is usually equivalent to "2 * 4 + 3"
A way around this could be by determining the precedence of each operation and then matching it to an operation of the same precedence in the other set of code. Once a set of operations have been matched, you can replace them with a variable to represent them.
Ex.
(2+4) * 3 + (2+6) * 5 == someotherequation
//substitute most precedent: (2+4) and (2+6) for a and b
... a * 3 + b * 5
//substitute most precedent: (a*3) and (b*5) for c and d
... c + d
//substitute most precedent....
These are just a couple ways I could think of. If you do it this way, it'll end up being quite a big project... especially if you're working with multiple languages.