How does OS 3.9 run on a stock A1200?
It doesn't. You need at least 6MB RAM.
To provisorily connect a CD drive should not be too difficult. You need a 2.5" to 3.5" adapter and a power cable. However you need to leave the case open and the drive lies uncovered on the table.
Another possibility is to connect the Amiga HDD to a PC and use WinUAE to install the OS.
Bye,
Thomas