How to repair or set up a Windows disk to be solo-bootable from another Windows install?

How do you repair a hard drive containing a Windows 7 Professional x64 install to be bootable on its own from within another W7 Pro x64 environment?

As explained below, I caot boot into most (Windows-based) recovery environments while the disk is plugged in, so the usual methods won't work.

After having some computer issues (still ongoing) I installed Windows on a fresh hard drive. After a while I needed to boot into my previous Windows installation, but having it as a secondary disk and booting to the new disk broke the bootloader ("Bootmgr is missing, press Ctrl+Alt+Del to restart").

I swapped drives around until it fixed itself, but the Windows logo was taking much longer than it usually does, so I shut the computer down. I unplugged all other drives and it did boot (albeit much slower than usual) at which time chkdsk popped up and scaed some partition (either the system reserved partition or the primary partition, I don't know). This scan went much quicker than I'd expect it to on a 1TB drive, so I suspect it was for the 100MB system partition. Then chkdsk failed with "unspecified error".

I restarted again, and this is the current situation: That install either never gets past the Windows logo, or bluescreens after a long time. The startup repair utility just hangs at a black screen. A Windows 7 Pro x64 installation disk (for repairing) either hangs at a black screen, or shows a cursor on a black background indefinitely.

I tried booting to boot-repair-disk and it took a few tries (and a while) to boot successfully, and didn't fix the issue, but at least now I'm back to getting "Bootmgr is missing" rather than a neverending Windows logo.

Physically the disk appears to be fine: I can hot-mount it in aforementioned Windows install and copy files from it with no issues.

Here is an excerpt of boot-repair-disk's failsafe boot log. This block of lines would repeat one or more times before it successfully booted:

ata1.00: exception Emask 0x0 SAct 0x100 SErr 0x400001 action ox6 frozen
ata1: SError: { RecovData Handshk }
ata1.00: failed command: READ FPDMA QUEUED
ata1.00: cmd 60/08:40:18:01:00/00:00:00:00:00/40 tag 8 ncq 4096 in
         res 40/00:00:00:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
ata1:00: status: { DRDY }
ata1: hard resetting link
ata1: SATA link up 6.0 Gbps (SStatus 133 SControl 300)
ata1.00: configured for UDMA/133
ata1.00: device reported invalid CHS sector 0
ata1: EH complete

Here are some relevant snippets from the log shown after boot-repair-disk did its thing. Irrelevant info or info about the Linux repair environment itself is omitted. There may be typos; I had to manually type it from a photo:

========================= Boot Info Summary: ===============================

sda1:

File system:      ntfs
Boot sector type: Windows 7/2008; NTFS
Boot sector info: No errors found in the Boot Parameter Block.
Operating System: 
Boot files:       /bootmgr /Boot/BCD

sda2:

File system:      ntfs
Boot sector type: Windows 7/2008; NTFS
Boot sector info: No errors found in the Boot Parameter Block.
Operating System: Windows 7
Boot files:       /Windows/System32/winload.exe

========================= Drive/Partition Info: ===============================

Drive: sda

Disk /dev/sda: 1000.2GB, 1000204886016 bytes
255 heads, 63 sectors/track, 121601 cylinders, total 1953525168 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes

Partition   Boot   Start   Sector      End Sector   # of Sectors   Id   System

/dev/sda1                   2,048        206,847         204,800    7   NTFS / exFAT / HPFS
/dev/sda2   *             206,848  1,953,521,663   1,953,314,816    7   NTFS / exFAT / HPFS

"blkid" output:

Device      UUID               TYPE      LABEL

/dev/sda1   7EAC921BAC91CE51   ntfs      System Reserved
/dev/sda2   3EDC9458DC940BF1   ntfs
/dev/sr0                       iso9660   Boot-Repair-Disk 64bit


ADDITIONAL INFORMATION:

$MFTMirr does not match $MFT (record 0).
Failed to mount '/dev/sda1': Input/output error
NTFS is either inconsistent, or there is a hardware fault, or it's a
SoftRAID/FakeRAID hardware. In the first case run chkdsk /f on Windows
then reboot into Windows twice. The usage of the /f parameter is very
important! If the device is a SoftRAID/FakeRAID then first activate
it and mount a different device under the /dev/mapper/ directory, (e.g.
/dev/mapper/nvidia_eahaabcc1). Please see the 'dmraid' documentation
for more details.
mount /dev/sda1 : Error code 13
mount -r /dev/sda1 /mnt/boot-sav/sda1
$MFTMirr does not match $MFT (record 0).
Failed to mount '/dev/sda1': Input/output error
NTFS is either inconsistent, or there is a hardware fault, or it's a
SoftRAID/FakeRAID hardware. In the first case run chkdsk /f on Windows
then reboot into Windows twice. The usage of the /f parameter is very
important! If the device is a SoftRAID/FakeRAID then first activate
it and mount a different device under the /dev/mapper/ directory, (e.g.
/dev/mapper/nvidia_eahaabcc1). Please see the 'dmraid' documentation
for more details.
mount -r /dev/sda1 : Error code 13
Windows not detected by os-prober on sda2.

========================= os-prober:
/dev/sda1:Windows 7 (loader):Windows:chain

========================= PARTITIONS & DISKS:
sda1 : sda, not-sepboot, no-grubenv nogrub, no-docgrub, no-update-grub, 32, no-boot, is-os, not-e<cut off>
sda2 : sda, not-sepboot, no-grubenv nogrub, no-docgrub, no-update-grub, 32, no-boot, is-os, not-e<cut off>

========================= parted -l:

Model: ATA WDC WD1003FZEX-0 (scsi)
Disk /dev/sda: 1000GB
Sector size (logical/physical): 512B/4096B
Partition Table: msdos

Number  Start    End    Size    Type    File system  Flags
1      1049KB  106MB   105MB   primary  ntfs         boot
2      106MB   1000GB  1000GB  primary  ntfs

========================= Recommended repair
The default repair of the Boot-Repair utility will restore the [(generic mbr)] MBR in sda, and make it boot on sda2.
Additional repair will be performed: unhide-bootmenu-10s repair-filesystems fix-windows-boot

Force Unmount all blkid partitions (for fsck) except / /boot /cdrom /dev /etc /home /opt /pas /proc /rofs /sys /tmp /usr /var

ntfsfix /dev/sda1
Mounting volume... $MFTMirr does not match $MFT (record 0).
FAILED
Attempting to correct errors...
Processing $MFT and $MFTMirr...
Comparing $MFTMirr to $MFT... FAILED
Correcting differences in $MFTMirr record 0...OK
Correcting differences in $MFTMirr record 1...OK
Correcting differences in $MFTMirr record 2...OK
Correcting differences in $MFTMirr record 3...OK
Processing of $MFT and $MFTMirr completed successfully.

ntfsfix /dev/sda2
Refusing to operate on read-write mounted device /dev/sda2
Quantity of real Windows: 1
Will restore the MBR_TO_RESTORE : sda (generic mbr) into sda
dd if=/usr/lib/syslinux/mbr.bin of=/dev/sda
0+1 records in
0+1 records out
parted /dev/sda set 2 boot on

Information: You may need to update /etc/fstab.

Boot successfully repaired.
You can now reboot your computer.