Since I can't use floppies (for some reason), maybe I can install WB3.1 to a HDF image under WinUAE, then copy that HDF to my cf card, copy a start up disk with drivers for cf0: to RAD:, boot off that, format HD0:, mount HDF image, copy contents to hd0: and be happy?
Why make things complicated?
In WinUAE, you can mount a RAW device directly as device for the emulated Amiga system. Thus, plug in a CF Card reader to your PC, put in the CF Card (unformatted) and just mount it as RAW in WinUAE; You can boot then Workbench from the ADF images and install to the CF Card as you would do on a real Amiga (including partitioning etc.), then simply put the CF card in your real machine and it boots like it's always been in there

Also, i usually keep a image of that card, by adding a "File HDD" as DH1 and copy everything from DH0 to DH1 in case i need to restore the original status. Lately I've started working on my installations on the File HDD in WinUAE and copy it when iam done with my updates/installing stuff, but either way should solve your problem way more efficient then the method you described above.
Good luck!
- G