1. First see if you can get the use cases, I.e. what are the requirements for the system. 2. Choose 1-3 core use cases. Analyse those use cases - Data in / Processing / Data out. 3. Draw UML diagram of the components in the systems. 4. Trace each use case end to end with either a debugger or just code reading. 5. Along the way, draw UML diagram of the class / data structure. 6. For each class add the core methods where all the business logic resides.

BTW thousands line of code is NOT a big code base.