easy.
remove the 2.1gb HD
make sure that the 40gb and the cd work fine together
boot from the Emergency Disk and have the 3.9 CD on the dc-drive
go to HDToolbox to partition the 40gb hd, but make the 1st boot partition SMALLER than 2GB (make it 1.9GB for example...) you can make the rest partition whatever size you like...
now install the OS from the cd on the 1st partition and you are set!
EDIT: to make an emergency cd, boot with the 2.1gb hd that has OS and insert there the 3.9 cd, open the installer and choose: Create Emergency Disk (if it asks about cdrom driver, tell it to copy it also)