I suggest you return it specially if you are planning to run an OS on it, definitely not the way to go with that drive. While it doesn't state the RPM anywhere on the label, it spins at about 52000 RPM which is not what you want if you are looking for performance. I just bought one a week ago (actually a 1.5 TB WD15EARS) during an impulse buy and it has been just awful, I have older PATA drives that run faster, an couldn't return it to the store since I threw away the label anyways, I'm selling it to a friend who only needs it for storage at about 40% off and getting myself a 1 TB SAMSUNG Spinpoint F3 instead, for what I read on reviews that's the best kind of performance you are going to get for about the same price, so I'm hoping that will do it.
While there might be a "fix" to increase speeds, setting the jumpers etc I wouldn't hold my breadth on it. This drives are designed to run on low power and mainly used for storage.
The WD Greens are designed for low power, not for speed - but they can certainly do a lot better than ~40MB/sec. The WD10EARS drive I have often goes up to 90MB/sec. I've used it as the OS drive during the Windows 7 beta period and it was perfectly adequate. A 45-minute installation sounds reasonable off the top of my head.
Regarding alignment - the most important thing is that the partition on the drive was created under Windows 7. If the partition was created by an older operating system and you installed Windows 7 into it, you're going to have a problem. If that's the case, then re-install Windows 7 and during the installation delete ALL of the partitions and then re-create them. If you do that then the partition should be aligned and it should work at peak performance.