Heh!  Me either.  I ran the check4gb program, copied its output to my PC, then copied it into my post here, and in not one of those operations did I notice it said G instead of M for DH1.  Obviously that's impossible since the entireSD card is only 16 GB.  I'd say 
excellent catch, Thomas!
So I repartitioned DH1 using the 3.9 HDToolBox and made it smaller this time, and ran check4gb again.  Now it shows:
Name     Volume       Size Device       Unit Version  DosType  Version   Big Check
DH1                   985M gvpscsi         0 3.7      DOS1     45.9       no ok
DH0                  4030M gvpscsi         1 3.7      DOS1     45.9       no ok
QDH0     QDH0        2169M gvpscsi         2 3.7      DOS3     45.9       no ok
SDH1     FS5         2047M gvpscsi         3 3.7      DOS3     45.9       no ok
EMERGENCY_CD AmigaOS3.9   512M gvpscsi         6 3.7      CD01     42.19      no ok
DF0      Emergency-Disk   880K trackdisk       0 40.1     DOS0     45.9       no ok
DF1      AsimCDFS_v3_Instal880K   880K trackdisk       1 40.1     DOS0     45.9  
Then I formatted DH1 as FS3, did a complete install of 3.9 from the CD-ROM and CTL-A-A rebooted.  This time FS3 booted fine with no gurus, WB reported 45.1, and AmiDock started without errors.  Then I tried installing BB1.  That worked fine too.  No complaints about the CD-ROM, everything installed fine.
So I rebooted, installed BB2 and rebooted again.  This time I got a yellow "Recoverable error" box.  I clicked left and got the error again.  I clicked left again and then it booted into FS3 correctly.  I tried a cold boot and got the same error.  So what's up with that?  FWIW I said Yes when BB2 offered to update my Amiga OS ROM Update.  Was that a mistake?  Here's the log:
******* Installation Log *******
User Level: AVERAGE
Pretend: No
>On which partition should Boing Bag 2 for AmigaOS 3.9 be installed?
Ask Drawer: Result was "FS3:".
Run Program: "C/Version "FS3:Libs/xadmaster.library" FILE VERSION 10"
>
>BoingBag 3.9-2 contains a new AmigaOS ROM Update. Although it has been
>tested thoroughly it may fail on some hardware configurations. Do you
>wish to install it?
>
>IMPORTANT: Please REALLY read the help text. ROM Update is provided with
>only limited warranty and support! Neither Amiga Inc. nor HAAGE&PARTNER
>are obliged to make sure that it will work on your system. Please also
>read the Readme file.
>
>The AmigaOS ROM Update is installed on your system. So generally, it
>should be safe for you to update it.
Ask Question: Result was "Install ROM Update".
Run Program: "C/Updater AmigaOS-Update "FS3:""
Run Program: "C/Updater XAD-Update "FS3:""
Copy file "FS3:Devs/AmigaOS ROM Update" to "FS3:Devs".
Copy file "FS3:Devs/AmigaOS ROM Update.BB39-2" to "FS3:Devs".
Copy file "C/Installer" to "FS3:C".
Copy file "C/Installer" to "FS3:Utilities".
Run Program: "C/RemoveResident"
Exiting script...
In any event aside from that things are looking much better now.