yes, R60 and R43 is what you are looking for.
Strange enough, it seems WD finally corrected the bad pcb layout they have been using for 10 years and decided to protect the circuit instead of the TVSes.
And why you measured D1 as shorted before removing D3: it was simply because they are wired in paralel, which means you can't really decide which one is shorted until you remove one of them.

@mordros, I would clean up the solder splash around D3.

After you sort out R43, I would also clean the HDA contacts.

Oxidisation on Western Digital PCBs:
http://www.hddoracle.com/viewtopic.php? ... 649&p=1789

If you wish to test the onboard power supplies, let me know. Otherwise I would power up the board off the drive to ensure that all is OK.

BTW, the unpopulated locations at U4 and U3 have been reserved for STEF12 and STEF05 electronic fuses. Just today I've been looking at a Seagate ST3000DM001 PCB with an unpopulated 5V e-fuse, so it looks like we might be seeing them in future.