For AmigaDOS partitions, there's really no need to do a dd-style sector-by-sector copy. I'd suggest just prepping the partitions on your CF card how you like and then copying the files using
copy oldrive:#? newdrive: all clone or DOpus. And you could do everything under WinUAE using a better partitioning tool and a full Amiga environment and then just plug the CF card back into the Dataflyer when you're done with everything (the Dataflyer does support the RDB standard, right?).
For your non-AmigaDOS partitions, I recommend the dcp tool from
this package. It's been a while since I used it, but it does essentially the same thing as dd but with Amiga-like syntax. Assuming your new partitions are an exact match to the old ones, everything should be fine. Might take a few tries to get it right - make sure to keep backups of everything until you know you've been successful. I'm guessing they're Mac or PC partitions for emulation?
EDIT: Oh, sorry, missed the part about there being errors on the disk that you need to ignore... Hmmm... Well, if you use DOpus you'll at least be able to continue from where the copy job halted, but I think you will have to manually intervene each time an error comes up... Hopefully someone else has a better idea...
