Backups via PCMCIA are really slow, it's no good for large amounts of data as you have found.
Best option for this kind of backup would be an accelerator with SCSI such as the Blizzard 1230MkIV + SCSI kit & external drive in case but I see you already have a nice ACA1231.
So in your case my advice would be to mount the CF card by the rear expansion slot for SCSI or under the trapdoor in the space left from the ACA using longer IDE cable then you can easily remove the CF and backup with WinUAE in Turbo Mode.
Once you have your backups on the PC it's much easier to restore and prep future CF's too.
There are also CF-IDE adapters that you can mount above the PCMCIA slot (requires that you file the slot out a bit though)
This will mean you can have access to the CF all the time
http://eab.abime.net/showthread.php?t=57678