Okay, for the SSD stalls (MAY work on non SSD, harmless to try anyway, can always turn it back on).
Start->Control Panel->Hardware and Sound->Device Manager->IDE ADA/ATAPI Controllers
Now from here your entries for the ATA controllers will be named specific to your hardware. Mine are "NVIDIA nForce Serial ATA Controller". I have three, click each one and then click on the Port0 or Port1 tab to find the drive you want to disable NCQ on. Then just unclick the Enable Command Queing.
Reboot and see if the pauses go away. If not, turn it back on, if so good to go. One annoying side effect of this is that the W7 speed rating test will no longer work