Repairing Bootcamp after new partition

You have a different issue. You have an extra partition with El Capitan. Is that intentional?

We can make this work, but you need to backup Windows very well, otherwise you will lose your data.

Can you post the output of

sudo dd if=/dev/rdisk0s5 count=1 2>/dev/null | hexdump -C

El Capitan SIP can cause you issues in the future - About System Integrity Protection on your Mac - Apple Support .

The following steps are non-standard because there is a third user-visible partition. Typically, there are two such partitions in a normal configuration on a single-disk Mac with OS X and Bootcamp. This is fragile and lack of proper backups can lead to potential data loss. Download GPT Fdisk from http://sourceforge.net/projects/gptfdisk/ and install it on the OS X side. The following steps are executed when booted in OS X. If you delete El Capitan in the future, these numbers (3 4 5) will change back to (2 3 4). You will lose visibility to OSX partition from Windows side.

Rebuild MBR to match the new GPT information thus resetting the Hybrid MBR. Use defaults for other questions (like partition codes). The only values that need modifications are the Boot flags and step 10. Accept all other defaults that Gdisk offers. Please see thesample Q&A as an example. These steps can be repeated if you make a mistake before you get to Step 12, otherwise start from Step 1 for these steps. Step 6 has numbers which are typed with a space between the numbers. Please see the sample Q&A before you execute these steps.

1. Sudo gdisk /dev/rdisk0
2. P (Print list of parts)
3. R (Recover)
4. O (print current Hybrid MBR)
5. H (chooses Hybrid)
6. Partitions numbers to be hybridized: 3 4 5
7. Y (Good for GRUB question)
8. N (part 3 boot flag)
9. N (part 4 boot flag)
10. Y (part 5 boot flag make NTFS bootable partition)
11. O (print current Hybrid MBR)
12. W (Write the new MBR)
13. Y (Yes! write the new MBR)
14. Reboot

Here is sample Q&A for this section. Please notice the Press Enter/Return. Accept defaults offered by Gdisk.

Place EFI GPT (0xEE) partition first in MBR (good for GRUB)? (Y/N): Y

Creating entry for GPT partition #3 (MBR partition #2)

Enter an MBR hex code (default AF or AB): Press Enter/Return

Set the bootable flag? (Y/N): N

Creating entry for GPT partition #4 (MBR partition #3)

Enter an MBR hex code (default AB or 0B or 0C): Press Enter/Return

Set the bootable flag? (Y/N): N

Creating entry for GPT partition #5 (MBR partition #4)

Enter an MBR hex code (default 07): Press Enter/Return

Set the bootable flag? (Y/N): Y

No worries. Please post back if you run into any issues with the steps or things do not work.