it has been a few months and I have some updates on this issue:
4. Even if the drive is fully ejected, OS X does not spin down the drive when it wakes up from sleep. To workaround this bug, I used Sleepwatcher to execute the eject command whenever OS X wakes up from sleep. I can write up a tutorial if any one is interested.
Come to think of it this might solve some of my issues too. For some reason when I wake from sleep it spins up, then spins down after the time delay, but then starts spinning again for no reason. A manual eject works too but like had2B said automatic would be awesome!
And yeah no Parallels on this computer.