The +1.2V and +3.3V supplies are probably the Vcore and Vio supplies for the MCU and SDRAM. These are controlled by the motor controller combo IC at U1. L2/D2 and L1/D1 appear to be the inductors and Schottky flywheel diodes (not TVS diodes) for two switchmode DC-DC converters. One supply should be the Vcore, the other will be the Vio. To determine which is which, test for continuity between the inductors and the test points. Obviously both diodes are OK.
I'd also measure the voltages on each of the pins of transistor Q1, and I'd also probe the voltages at the preamp connector. The pins with the heavier traces should be the preamp supply pins, and the two ends of the voice coil.
Is the drive identified by your BIOS? If so, then it could be that your drive is configured to Power Up In Standby (PUIS). PUIS can be enabled either via an ATA command, or via a PM2 jumper.
WD Jumper Settings Guide:
http://www.wdc.com/en/library/eide/2579-001037.pdfhttp://www.jerryching.dyndns.org/Web%20 ... etting.gif