I am getting a weird issue here....I do not have the CD interface for my 1200, so I am using the PC to install 3.9 on my CF card.
The partitions seems fine, I tried to boot from Install disk, and I can see the drives and contents of the various partitions. But when I put the CF card in the Amiga, it just goes in guru, as soon as it boots, the power light blink and it restart.
It seems to work just fine on WinUAE.
This is what I did: Installed 3.1, updated to 3.9, installed ClassicWB for 3.9, installed some applications (like assembler, WHDLoad, Dpaint and so on).
Is there something that I can do to troubleshoot the issue, or do I have to start all over, installing 3.1 -> 3.9 -> MagicWB -> software; and see in which stage it stops?
I miss the nice modern crash reports 
Most likely your boot partition is unreadable on the real Amiga. It must be smaller than 4GB and completely inside the first 4GB of the drive.
To emulate the same behaviour in WinUAE make sure the drive is connected to IDE0 controller, not to UAE controller.
If you want to make one 8GB partition which is bootable, you have to use a third-party file system, either PFS3ds, PFS3aio or FFSTD64.