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I'm not sure what I'm supposed to do here.

For some background knowledge, my late 2011 Mac does "not have UEFI firmware and the ability to boot Windows installers from USB flash drives until the 2012 model year."

Therefore I am following the guide here: Boot camp install of Windows 7 issue, no bootable devices

Essentially, I'm transferring a Virtual Machine to a hard drive partition, in this case a fresh Windows installation. I failed to install Windows 8.1 the first time because I ended up running the wrong bootcamp drivers, which resulted in blacking the screens out (Graphics drivers probably failed). I decided to remove the partition my merging it back with my original El Capitan partition.

In the guide, it mentions:

If your partition number is greater than 4, then you can not install Windows on this partition. (Technically, this may not be true, but it is beyond the scope of this answer to explain how to do so.)

Unfortunately, that is the exact problem I have; how do I get my partition to be a number less than 5?

Any help is greatly appreciated! Thank you.

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For your model Mac, OS X maintains two different disk partition tables. First is has the name "Master Boot Record Partition Table" or the abbreviated name MBR table. The second is called the "Global Unique Identifier Partition Table" or the abbreviated name GPT. The MBR table can only have 4 entries, where as, the GPT can have 120 entries. When OS X makes an entry in the MBR table, the entry is also duplicated in the GPT. Furthermore, these duplicates are stored in both tables using the same index. For example, if an entry is duplicated and one of the pair is the 3rd entry in the GPT, then the other will be found as the 3rd entry in the MBR table. This means any GPT entry with an index greater than 4 should never appear in the MBR table.

While OS X is aware of both the MBR table and the GPT, the same is not true for Windows. For you model Mac, Windows will never look at the GPT. It only sees the MBR table. If you used OS X to create the Boot Camp partition with an index of 5, then this partition will not appear in the MBR table. Therefore, Windows will not be able to find this partition during the installation process.

It is possible to make the 5th entry in GPT be paired with one of the last 3 entries in the MBR table. This requires either a third party tool or a great deal of manually editing of the MBR table using the OS X command line tools. Ron Smith offers a third party tool called gdisk which can make this kind of change to the MBR table. Basically, you first select the r option to enter the "recovery & transformation" menu. Next, you select to h option to create a hybrid MBR. At this point, you can enter the indices of the GPT partitions you what to appear in the MBR table. Finally, you select the w command to write the changes to the MBR table on your drive.

If you wish confirm if the use of gdisk would help install Windows on your Mac, then edit your question and add the output from the following commands.

sudo fdisk /dev/disk0
sudo gpt -r show /dev/disk0

These commands will not change your Mac. They may ask for your login password. This is normal. The GUID's produced are all published in the public domain. A list of these GUIDs can be found here.

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