Not sure on this, but you might be able to use the importprivkey RPC call. What I would try is importing one of them with rescan=false and then import another with rescan=true. The rescan=true causes it to go through the whole blockchain and look for any places that the associated address to that private key. After importing two private keys, the first without a rescan and the second with a rescan, then look to see if rescanning on the second private key got you all the transactions for the first private key that you entered.
Then if that works, you could write a command line script to execute that RPC call with each line of the file as the private key.
That's a high level description of what I would try. If you need more help on the importprivkey, open the Bitcoin-QT GUI, go to Help >> Debug Window >> Console and type "help importprivkey". If you need help writing that script, you'll probably have to do some googling around to learn about your OS-dependent scripting language.