P1 & P2 are the connections to the ST-506 hard drive.
I can't remember what the Molex power connector was for (haven't seen a HyperDrive in a Mac for well over 15 years now!), but since the inside of the socket isn't dusty, it must have had a plug in it when it was in the Mac. As an educated guess, I'd say that it was for power for the board itself from the hard drive power supply. The HyperDrive had its own switchmode power supply mounted up inside the back half of the Mac case, since the Mac 512 power/Sweep board wasn't up to running an internal hard drive (especially not one of that vintage).
I can't remember what the Molex power connector was for (haven't seen a HyperDrive in a Mac for well over 15 years now!), but since the inside of the socket isn't dusty, it must have had a plug in it when it was in the Mac. As an educated guess, I'd say that it was for power for the board itself from the hard drive power supply. The HyperDrive had its own switchmode power supply mounted up inside the back half of the Mac case, since the Mac 512 power/Sweep board wasn't up to running an internal hard drive (especially not one of that vintage).