Changing the "system" partition

Before changing the system partition you'll need to do a bit of prep work. If the OS partition is located in a logical partition the partition will need to be converted to a primary. At present Microsoft does not have any tools out of the box to handle this. If you decide to use strictly Microsoft tools then go here (future reference).

First alter boot.ini as follows:

It should look something like this if you're booting the system from a logical partition:

Boot.ini after reinstall

Note the reference to partition(2). Simply duplicate all of the last line. By changing the name between the quotes you'll be able to identify which partition you're booting.

Suggested change to boot.ini

As another suggestion, change the timeout value to something a bit higher than 1 second.

Now copy boot.ini, ntdetect.com and ntldr from the root of the current system partition to the root of the boot partition. Since these are hidden system files make sure to change explorer folder options to display all files or you won't see them.

Since third party tools vary in the specifics of how they convert a partition to from logical to primary I'll forgo the details at the moment and simply assume the partition has been converted. Note that if you do not alter boot.ini in advance of the conversion you'll need to use use a tool such as BartsPE, EDBINI or the recovery console bootcfg command to correct it.

Note that you'll probably have to change the OS selection on the boot menu. Once you've finished the below steps you can alter boot.ini to default to partition(1). Or if you wish, you can alter boot.ini on both drives.

After you reboot the system post conversion diskmgmt.msc should look something like this:

Disk management after conversion

Notice that the boot partition is no longer marked as a logical volume. At this time you can right click the boot drive (in either window) and you'll have the option to mark it as active.

Mark partition active

 

You'll get a confirmation box:

Confirm change

 

And in this instance, just say yes.

Now reboot the system and get into recovery console. Run fixboot on the default partition as follows:

Fixboot on current system

The system should now boot solely from the "new" system partition. After the system comes up diskmgmt.msc should look something like this:

Disk management