I don't think the HD controller would be on the daughter board. The service manuals says to take these steps, in order, if the hard drive doesn't spin:

1. Make sure power adapter is connected.

2. Disconnect external devices.

3. Check hard drive connection.

4. Replace hard drive cable. Note: Pull up evenly on the cable to avoid bending pins.

5. Replace hard drive.

6. Replace I/O logic board.

It's a pretty safe bet that it's the logic board and your awesome G4 upgrade is okay.