I don't mean to use this forum to solicit work, but we have seen an awful lot of this thing over the past two years now that EIDE/ATA/Atapi is common to the Mac.
We offer data recovery for just this instance (as long as the drive spins) at a flat fee of $150 plus S&H (plus CD burns, if required); if your data value meets or exceeds that amount, please contact me at the address below.
That said, if you want to take a few shots at it yourself, try the following:
1) Jump the unseen drive(s) as Single and move them to a single or dual-drive cable on the second bus (ID 0 bus 1). Be sure that the blue connector on the ATA 40/80 ribbon is on the MOBO and the black is on the drive. Do *not* use a standard ATA-40/40 ribbon cable. Connect no other devices to the machine on either bus, including FireWire and USB.
Remove the PRAM battery, hit the CUDA reset button (if present) and wait fifteen minutes. Repalce the battery, Startup, and see if it can find your original System Folder, and be patient. If the drive had no active System folder, or is still not seen (Flashing '?' for more than five minutes), power off and add the CD/DVD/Zip combo back, but this time on Bus 0 (you may need to remove the MOBO to make the cable reach, or use a spare ATA-40/80 cable, and, again, blue to MOBO, black (end) to Master/Single, and grey (center) to Slave. Startup again, and see if Drive Setup *v1.9.2*can see the drive. If yes, use the 'Mount' Command and then 'Update Driver' and Restart.
Repeat the procedure with the second drive, restore proper jumper settings (be certain you use the Master with Slave Present settings; Mac does not support DSP) and cable connections to the original bus; live happily ever after.
2) If the above doesn't work, jump the drive(s) as Single again, and install them in a '98 or earlier G3 Mac (or Performa) that has an original EIDE (ATA-8;16) controller, and use the old-style EIDE-40/40 ribbon as a single ended device. Do **NOT** install the damaged drive as a Master or Slave to any other known-good drive, you'll whack it, too.
Use another device on the second EIDE (if present) or any SCSI bus, or even the floppy drive to boot the machine; if the drive does not mount automatically, use Drive Setup *v.1.9.2* to 'Mount' and 'Update Driver'.
Reinstall in your G4 and live happily ever after.
3) Failing the above, contact me at the address below; your data is alive and well, the Mac just can't see it.
HTH
Frederico
frederico@mac.com