"BOOTMGR is missing" error - I've tried almost everything

First, let me give you a little background. I purchased this computer (a Lenovo Y-580) about two weeks ago, and have been using it for about a week. When I first got it, the hard drive it came with wouldn't boot so I put in another one I had left over (I upgraded my hard drive a while ago). Little did I know, was that that I forgot to erase that hard drive cleanly, so when Windows 7 installed, it resulted in both an MBR partition table and a GPT partition table at the same time. I discovered this when I went to install Ubuntu (with the cinnamon UI) on the secondary drive that came with my computer (a 16 GB SSD), and I noticed that the partition map for the drive that I wasn't installing on looked wrong, so I put it on my to-do list to look at later. I booted into Ubuntu and pulled up Testdisk and Gparted. Gparted was acting strange, asking me if the GPT table was correct (it wasn't), and I clicked no since I was positive it was MBR and Gparted wouldn't display any partitions. I went in Testdisk and set the type to Intel/PC. I then scanned for partitions, found one, and wrote the MBR. Of course this didn't do anything, because for some reason the GPT table was not being overwritten at all. I then resorted to erasing the entire MBR and making a new one. I figured that I could always use bootrec to fix it. Nope... After 8 hours of on and off trying to fix this problem, it still gives the same error. I've tried bootrec, bootsect, and various other commands, in addition to Startup repair and Hiren's boot CD. I've also tried setting the partition to active using diskpart. Not a single one has worked. Even a wipe of both the C:/boot folder and the MBR and then re-writing it from scratch doesn't work. I recently spent an entire day getting my computer set up exactly the way I want it, I don't want to have to re-do it. Can anyone help?

Unplug all other HD's and peripherals to install Win7 first. Afterwards you can unplug the Win7 HD to install Linux, so that you will boot your choice of HD's via the BIOS which avoid problems.

Boot into BIOS setup, reset to defaults, save changes. Next if an EFI BIOS, enable Legacy BIOS, set DVD drive first to boot, HD second. Then set SATA controller to AHCI. Save changes and Exit.

Then boot into installer DVD or flash stick burned or written using tool and latest ISO for your licensed OS version here.

At first installer screen Press Shift + F10 to open a Command Box, type:

DISKPART
LIST DISK
SELECT DISK 0 (after confirming Windows 7 target HD #)
CLEAN
CREATE PARTITION PRIMARY SIZE=102400 (for 100gb partition, adjust as desired)
FORMAT FS=NTFS LABEL="WINDOWS 7"
ACTIVE
EXIT
EXIT

Next click Install Now, then Custom install to Clean Install Windows 7 to the partition you created. If it fails then report back at which step and the verbatim error message.

In addition read over these steps to understand the tools and methods which work best to get and maintain a perfect Clean Reinstall - Factory OEM Windows 7. The steps are the same for retail.

After install you can adjust partition size or Create new partitions for data, etc. in Disk Mgmt. We are creating the partition here to mark it Active which overcomes certain install failures.

gregrocker said:

Unplug all other HD's and peripherals to install Win7 first. Afterwards you can unplug the Win7 HD to install Linux, so that you will boot your choice of HD's via the BIOS which avoid problems.

I don't mean to be rude, but that doesn't solve my problem. Doing a clean install is not an option. If I can get it to boot and do a repair install, that would be OK, but I can't get it to boot without a boot manager. Do you know of any way to get around that?

How do you know the steps I gave won't solve your problem? Those steps combine the most effective fixes to a number of install issues which affect you based on tens of thousands we've helped with successfully here which has made us the top site on the web for this.

GPT/MBR with a questionable or failed install is easiest converted by running the Diskpart Clean command, which also wipes the boot sector of code that can conflict.

You may also have an EFI BIOS if GPT disk came with PC which it's hard to decipher from your jumble. The steps I gave make it easiest for installing a dual boot with Ubuntu in that case by bypassing EFI to install both to an MBR disk.

And it's always best practice to unplug the other HD when installing a Dual Boot so that problems are avoided, especially GRUB. Otherwise you can consider this method: Dual Boot - Windows 7 and Linux - Windows 7 Forums

Why is reinstall not an option? You said yourself you bought a factory OEM PC which wouldn't boot, have a mess which can't be easily sorted. You are the perfect candidate to get a perfect Clean Reinstall - Factory OEM Windows 7. This is an install vastly superior to the bloatware which comes preinstalled from the factory.

But if you want to continue wasting time with your failed install everything that can be done to start unbootable Win7 is in these steps for Troubleshooting Windows 7 Failure to Start