Hello,
I assume you have the 3.1 roms fitted? Otherwise OS3.9 will not boot.
Here's how to get OS3.9 booting on your system:
1 Run tools:hdtoolbox
2 Go to "Partition drive".
You are now looking at the aprtitions on your hard drive.
3 Click on dh1:
4 There is a box (at the bottom, near the middle) with "make partiton bootable" next to it. Tick the box.
5 On the same screen set the boot priority to 2.
6 Save and exit.
7 Reboot.
PS - welcome to Amiga.org :-)