There is something "queer" in the "custom" install.
From what you report it seems like the Windows 7 install "decided" that the first partition was it's own "boot" partition (what MS calls "System) , and that the second partition is the windows 7 "System" partition (what MS calls "boot"), see here:
for the misnaming.
If you open Disk Management, you should be able to see the first partition alright, only it will have NOT a drive letter attributed.
You can manually assign a drive letter to that first partition, let's say that you assign to it "F:".
In theory it is possible to change the drive letter assigned to the second partition from the current "C:" to "D:", but in practice it is extremely complex and very much error prone (besides the procedures needed not having been tested or tested enough).
For these reason it is STRONGLY NOT advised to attempt doing it.
What you can do, once you have found which of the two partitions (I tend to believe first one) contains the files \BOOTMGR and \boot\BCD, is to create a DOS bootsector file for it and add to it a good ol' BOOT.INI file invoking that file.
To create the DOS bootsector (BTW which version of DOS?) there are a couple utilities available, while the BOOT.INI can be written with Notepad alright.
should be able to create the bootsector in file directly (and run on 7 too).
As well MBRFIX will be able to create the bootsector (and surely runs under 7):
but it can only update the "real" bootsector, so you will need another tool, like the dsfo of the dsfok toolkit:
to extract it to file (and then re-use MBRFIX to restore the Windows 7 bootsector).
The BOOT.INI should be something like:
C:\DOS\BOOTSECT.DAT="Microsoft DOS version x.xx"
This way DOS will become an entry in the BOOTMGR choices.
Or you can use a bootmanager like grub4dos.
If you wish to always boot to DOS and from it launch Windows 7, you can also use grub.exe (still part of grub4dos).
Since DOS is unaffected by the Windows 7 drive lettering (and in any case it won't be able to see/access the Windows 7 partition, which I presume is NTFS), when you boot to DOS you will see only a drive letter/partition (C:\) corresponding to the first partition and when you boot to 7 you will see instead the second partition as C:\ and you can assign to the DOS partition any other letter.