I think it's "Build/Strategic/Game_Init.cc"
Look for "cash" in this file to find where the starting funds are allocated.

The "Finances" screen and most of the money functions are in "Build/Laptop/Finances.cc".
Look for function names like "GetTodaysBalance()" to find the variable in which your money is stored. Its name is something like "LaptopSaveInfo.Balance".

All the money changes are written in the file "finances.dat" somewhere in "$HOME/.ja2/data/...". I think it's "$HOME/.ja2/data/temp/finances.dat" but I'm not sure. You can see this file only when you are playing. It's removed when you leave the game. Today's debits are guessed from all the other values written in this file. When you start a new game, I think its size is 18 bytes. The first 4 and last 4 bytes are your current money at this point.

I already ran a debugger on all of this and didn't notice anything interesting except (for info only) that all the read/write functions depend on your processor's endianness while I was wrongly led to think that they were endianness-independent, guessing from their names. But it's not related to your problem.