There are two possible solutions, but both run into a potential problem when you move the drive. Moving a drive will, at best, ruin any authentication/registration you might do. At worst, Windows will refuse to boot entirely on the new motherboard/processor combo, making it useless.
However, if you want to try it, there are two easy ways:
Get CloneZilla and just completely clone the existing install to the new drive. You can do it by partition or drive, and the MBR should be cloned along with all the data and settings. I've used CloneZilla to clone VMWare virtual drives to real drives before, as well as real to real, and it usually creates a working, bootable drive. It also tends to be pretty speedy. (Edit: You do have to boot into CloneZilla for this one, although I just use EasyBCD to boot directly from the ISO, which works great.)
Unplug the first harddrive, toss a Windows 7 install disc in and install on that second drive.
Given that you'd like to do it without rebooting (it'd be a lot easier to just do a boot-from-disc, but...), I'm going to recommend the following rather convoluted process:
- Create a VMWare (or other) virtual machine. Either use a virtual harddrive or mount your secondary HDD as the VM's only HDD.
- Install Windows on the VM. Any good VM program will allow you to mount a CD/DVD image (ISO) as a CD drive, and most allow you to boot from that in the virtual BIOS.
- You now have a working bootable copy of Windows 7. If you installed to a virtual disk, boot the VM into CloneZilla to copy it to any hard-drive you want, or even many.
Obviously you need to double-check legality, but those methods work just fine most of the time.