Fusion Drive - Lost space when resizing
To remove the useless second EFI (104.9 MB) and the deleteme partition (104.3 GB) and expand the CoreStorage volume to the full size you have to boot to Internet Recovery Mode.

Preparation:


Backup your Mac
Detach any external drive (especially your external Time Machine backup drive)
Restart to Internet Recovery Mode by pressing alt cmd R at startup. Booting to Recovery Mode is not conducive because the Recovery HD will be moved in one of the steps below. And you can't move a partition used as a boot volume.  

The prerequisites are the latest firmware update installed, either ethernet or WLAN (WPA/WPA2) and a router with DHCP activated.
On a 50 Mbps-line it takes about 4 min (presenting a small animated globe) to boot into a recovery netboot image which usually is loaded from an Apple/Akamai server.

I recommend ethernet because it's more reliable. If you are restricted to WIFI and the boot process fails, just restart your Mac until you succeed booting.

Alternatively you may start from a bootable installer thumb drive (preferably Yosemite or El Capitan) or a thumb drive containing a full system (preferably Yosemite or El Capitan). If you boot to a full system and login as admin you have to prepend sudo to execute special commands like gpt ...!


Remove the partitions 2nd EFI/deleteme and shrink the CoreStorage Volume Group


Booted to Internet Recovery Mode open Utilities → Terminal in the menubar and enter:  diskutil list to get the disk identifiers and diskutil cs list to get a CoreStorage listing. Below I assume that your main disks have the disk identifiers disk0 (here the HDD)/disk1 (here the SSD) and the CoreStorage Logical Volume disk3. Please modify the commands below according to your environment/findings.
First you have to remove the 2nd EFI/deleteme partitions:

gpt -r show /dev/disk0 #to get an overview


To remove a partition with gpt the disks (and all related disks like the inherent CoreStorage volume) have to be unmounted - first the CoreStorage Logical Volume and then the physical disks (SSD and HDD):

diskutil unmountDisk /dev/disk3
diskutil unmountDisk /dev/disk1
diskutil unmountDisk /dev/disk0
gpt remove -i 5 /dev/disk0 #remove the *deleteme* partition
diskutil unmountDisk /dev/disk3
diskutil unmountDisk /dev/disk1
diskutil unmountDisk /dev/disk0
gpt remove -i 4 /dev/disk0 #remove the *2nd EFI* partition

Then you have to first mount and then resize the Logical Volume Group:

diskutil mount lvUUID #lvUUID: the logical volume UUID


in your case:

diskutil mount E6FCA8F6-D6FF-4C0E-976C-1AD2ED107824


Sometimes you have to mount the PVs first:

diskutil mount /dev/disk0s2 #mount the physical volume of the CoreStorage Logical Volume Group
diskutil mount /dev/disk1s2 #mount the physical volume of the CoreStorage Logical Volume Group


Then resize the whole CoreStorage stack with:

diskutil cs resizeStack lvUUID size


in your case (assuming you want to "resize" Macintosh HD to 1024 GB):

diskutil cs resizeStack E6FCA8F6-D6FF-4C0E-976C-1AD2ED107824 1024g


If you get Error: -69720: There is not enough free space... use a slightly smaller size like 1023g or 1023500m.

Now the CoreStorage stack should be expanded to the full size of your Fusion Drive.




After failing to remove a Windows partition with the Boot Camp Assistant parts of the CoreStorage logical structures may be corrupted and the resizeStack command fails with an error. The only possible solution then is to rebuild the Fusion Drive from scratch and restore your system with your current Time Machine backup.