Secondary drive left plugged in during install

OK so an update. I tried getting screen shots from within the BIOS and couldn't do it. But I can tell you that now in the configuration for my UEFI/BIOS my SSD comes up as a boot option and well as the boot menu (how or why these are two separate things is beyond me). I still can't boot into Windows without the HDD plugged in.

Also, when I do try without the HDD, Nero Boot Loader 6.0 comes up with a DOS kernal, which then loads this program in console:

Driver Disk Preparer
Model Name: P67 Extreme 4 <--my mother board
Select Source
1 Generate the RAID/AHCI driver diskette for Intel P67 chipset.
2 Generate the AHCI driver diskette for Marvell SATA 3.0
3 Exit

I haven't tried options 1 or 2. I don't even know what this is for.

Maybe I can unplug my HDD and just try to repair or re-install Windows on my SSD? If I do that, then when I plug in my HDD, won't I have a problem with those boot loading files still on it?

Microsoft Windows [Version 6.1.7600]
Copyright (c) 2009 Microsoft Corporation. All rights reserved.
C:\Windows\system32>bcdedit /enum all
Windows Boot Manager
--------------------
identifier {bootmgr}
device partition=E:
description Windows Boot Manager
locale en-US
inherit {globalsettings}
default {current}
resumeobject {214fcf45-51fd-11e1-984e-fd8647f7836a}
displayorder {current}
{214fcf42-51fd-11e1-984e-fd8647f7836a}
toolsdisplayorder {memdiag}
timeout 30
Windows Boot Loader
-------------------
identifier {214fcf42-51fd-11e1-984e-fd8647f7836a}
device unknown
path \Windows\system32\winload.exe
description Windows 7
locale en-US
inherit {bootloadersettings}
recoverysequence {214fcf43-51fd-11e1-984e-fd8647f7836a}
recoveryenabled Yes
osdevice unknown
systemroot \Windows
resumeobject {214fcf41-51fd-11e1-984e-fd8647f7836a}
nx OptIn
Windows Boot Loader
-------------------
identifier {214fcf43-51fd-11e1-984e-fd8647f7836a}
Windows Boot Loader
-------------------
identifier {current}
device partition=C:
path \Windows\system32\winload.exe
description Windows 7
locale en-US
inherit {bootloadersettings}
recoverysequence {214fcf47-51fd-11e1-984e-fd8647f7836a}
recoveryenabled Yes
osdevice partition=C:
systemroot \Windows
resumeobject {214fcf45-51fd-11e1-984e-fd8647f7836a}
nx OptIn
Windows Boot Loader
-------------------
identifier {214fcf47-51fd-11e1-984e-fd8647f7836a}
device ramdisk=[C:]\Recovery\214fcf47-51fd-11e1-984e-fd8647f783
6a\Winre.wim,{214fcf48-51fd-11e1-984e-fd8647f7836a}
path \windows\system32\winload.exe
description Windows Recovery Environment
inherit {bootloadersettings}
osdevice ramdisk=[C:]\Recovery\214fcf47-51fd-11e1-984e-fd8647f783
6a\Winre.wim,{214fcf48-51fd-11e1-984e-fd8647f7836a}
systemroot \windows
nx OptIn
winpe Yes
Resume from Hibernate
---------------------
identifier {214fcf41-51fd-11e1-984e-fd8647f7836a}
device unknown
path \Windows\system32\winresume.exe
description Windows Resume Application
locale en-US
inherit {resumeloadersettings}
filedevice unknown
filepath \hiberfil.sys
debugoptionenabled No
Resume from Hibernate
---------------------
identifier {214fcf45-51fd-11e1-984e-fd8647f7836a}
device partition=C:
path \Windows\system32\winresume.exe
description Windows Resume Application
locale en-US
inherit {resumeloadersettings}
filedevice partition=C:
filepath \hiberfil.sys
debugoptionenabled No
Windows Memory Tester
---------------------
identifier {memdiag}
device partition=E:
path \boot\memtest.exe
description Windows Memory Diagnostic
locale en-US
inherit {globalsettings}
badmemoryaccess Yes
EMS Settings
------------
identifier {emssettings}
bootems Yes
Debugger Settings
-----------------
identifier {dbgsettings}
debugtype Serial
debugport 1
baudrate 115200
RAM Defects
-----------
identifier {badmemory}
Global Settings
---------------
identifier {globalsettings}
inherit {dbgsettings}
{emssettings}
{badmemory}
Boot Loader Settings
--------------------
identifier {bootloadersettings}
inherit {globalsettings}
{hypervisorsettings}
Hypervisor Settings
-------------------
identifier {hypervisorsettings}
hypervisordebugtype Serial
hypervisordebugport 1
hypervisorbaudrate 115200
Resume Loader Settings
----------------------
identifier {resumeloadersettings}
inherit {globalsettings}
Device options
--------------
identifier {214fcf44-51fd-11e1-984e-fd8647f7836a}
description Ramdisk Options
ramdisksdidevice unknown
ramdisksdipath \Recovery\214fcf43-51fd-11e1-984e-fd8647f7836a\boot.sdi
Device options
--------------
identifier {214fcf48-51fd-11e1-984e-fd8647f7836a}
description Ramdisk Options
ramdisksdidevice partition=C:
ramdisksdipath \Recovery\214fcf47-51fd-11e1-984e-fd8647f7836a\boot.sdi
C:\Windows\system32>

Kaktussoft said:

of course you have to set ssd as first boot device btw

In the BIOS? It is. In fact my HDD isn't even showing up now as a boot device. It's like it got replaced by the SSD, but still has the boot files.

Man this is a mess.

To everyone reading this post: If you want Windows to exist on one drive and use another for data, do NOT leave it plugged in on install.

Microsoft Windows [Version 6.1.7600]
Copyright (c) 2009 Microsoft Corporation. All rights reserved.
C:\Windows\system32>bcdedit /displayorder {current}
The operation completed successfully.
C:\Windows\system32>bcdedit /default {current}
The operation completed successfully.
C:\Windows\system32>bcdedit /delete {214fcf43-51fd-11e1-984e-fd8647f7836a}
The operation completed successfully.
C:\Windows\system32>bcdedit /delete {214fcf42-51fd-11e1-984e-fd8647f7836a}
The operation completed successfully.
C:\Windows\system32>bcdedit /delete {214fcf41-51fd-11e1-984e-fd8647f7836a}
An error occurred while attempting to delete the specified entry.
The system cannot find the file specified.
C:\Windows\system32>bcdedit/enum
Windows Boot Manager
--------------------
identifier {bootmgr}
device partition=E:
description Windows Boot Manager
locale en-US
inherit {globalsettings}
default {current}
resumeobject {214fcf45-51fd-11e1-984e-fd8647f7836a}
displayorder {current}
toolsdisplayorder {memdiag}
timeout 30
Windows Boot Loader
-------------------
identifier {current}
device partition=C:
path \Windows\system32\winload.exe
description Windows 7
locale en-US
inherit {bootloadersettings}
recoverysequence {214fcf47-51fd-11e1-984e-fd8647f7836a}
recoveryenabled Yes
osdevice partition=C:
systemroot \Windows
resumeobject {214fcf45-51fd-11e1-984e-fd8647f7836a}
nx OptIn
C:\Windows\system32>