Let's take this in parts.
1- You have 2 wallet.dat files. 1 on the old HDD and 1 on the new HDD
2- Backup those 2 files. For convenience name the backups wallet1.dat and wallet2.dat
3- Fire up your new system, navigate to your bitcoin data dir
and copy wallet1.dat there. Rename it to wallet.dat
4- Start your bitcoin client with the -rescan flag from the command line (bitcoin -rescan).
5- Wait for it to finish rescanning and you should see the coins on wallet1.dat.
6- Repeat steps 3, 4 and 5 for wallet2.dat