On most phones a factory reset does not clear the SD card, so you've been very unlucky!
If you were able to move system files to SD I guess your phone must be rooted. If so, if you were using a custom ROM you could just flash the ROM again, or if not you could flash a new custom ROM onto the phone.
The other option would be to reflash the phone with a new set of official system software.
To advise on either ROMs or official software we'd need to know what phone you have though. You could post again with more information, but it might be easier if you registered so that you could post in the main forum - that way more people will see it, and it's easier to have a two-way discussion.
There is one other option: if you have a card reader you could use file recovery software on a PC to see whether you can restore the lost data. The important thing is not to write to the card in the meanwhile, as that may overwrite something important.
Good luck!