This instruction has helped somebody else, so you too can try.

I think the problem is the kernel.

I would go back to Android (6.0) and start everything from scratch again. (Root, multirom, then install secondary roms.)

This is how I set up and use my Nexus 5:
(I mentioned Ubuntu Touch here because I started with that first, then I moved to Sailfish OS.)

1. unlock boot loader
- adb reboot bootloader
- fastboot oem unlock
2. root (Info)
CF-Auto-Root
3. MultiRom with Ubuntu Touch repo (Info and Info about multirom):
- install 1-MultiROMMgr_withUT.apk (multirom with UbuntuTouch repo) with adb (Info):
- adb install 1-MultiROMMgr_withUT.apk
4. reboot recovery and install:
- kernel: kernel_kexec_hammerhead_601.zip
- multirom recovery: multirom-20160207-v33-hammerhead.zip
5. reboot android, start MultiRom and install Ubuntu Touch
6. SailFish OS (Info):
- boot into recovery: Advanced -> MultiROM -> Add ROM
- Choose "SailfishOS" as ROM type.
- Choose first CyanogenMod ZIP and then SailfishOS ZIP. Click install.

I have uploaded all files to my storage and made them available for you. So you don't need to hunt them together from the websites I linked in as Info at each step. However, I recommend to read them to get an overview.

I usually use one of these twrps. (With the newer one you can install Ubuntu Touch but cannot flash a zip on a secondary from. With the older you can flash a zip on a secondary from, but cannot install UT.): TWRP_multirom_hammerhead_20150630 or TWRP_multirom_hammerhead_20160210

Thanks for all the great work!

I seem to have the same problem as LinuxLounge (and probably as iKevinES and monkeyisland who posted in the CM13 thread). I cannot boot my Nexus 5 with the 20160704-UNOFFICIAL 12.1 image linked here, it gets stuck on the boot logo.

I found another image which does work. However, when flashing the SFOS 3.4 image on top of that, it hangs on the boot logo again. Interestingly, when connected by USB on boot, my Ubuntu machine sees a phone device with the cryptic name "init debug in real rootfs", which it cannot access: "Unable to open MTP device “001,065”".

Could the issue be that I am not using multirom?

Apparently the single rom is indeed the problem--when using multirom with the files from the links above, it works without a problem.

I would like to install SailfishOS as single rom, however. If there is anything I can do to make that possible than I would love to help.

I think the problem is the kernel. That should be kexec. You may try to flash the kernel first then reboot into TWRP and then flash the android base and SFOS. (I've seen comments from a single from users about this rom worked for them too.)

I have spotted that some android apps (in this case Protonmail) do not see the internet connection on SFOS 3.3.0.16 (Rokua). I've tried versions 1.9, 1.10, 1.11 and 1.12 but with none of them can sign in. Has anyone experienced the same? Is there any solution?

@edp17

Does Protonmail need Google Play services?

Afaik protonmail doesn't require any google services. It works fine on my sony xa2 where there isn't any google stuff. (It also works fine in Anbox on the Pinephone.)

Yesterday, I've upgraded my Nexus 5 from SFOS 3.3 to 3.4. (Thanks for @mautz for creating a repo for this.) As the upgrade was a bit unusual, I thought to share my experience.

I had to repeat the upgrade about 5 times because every time I rebooted into the new system and reached the lock screen, a few seconds later the screen went black. The phone was accessible via ssh, just the screen remained black.
When that happened I deleted that from, copied the other working one and tried to upgrade again.
Finally, I identified that if I didn't let the android support to start at boot, that solved this issue.
As you may have other problems after the upgrade, I highly recommend doing a backup before you start.

The upgrade steps are defined in this post. I followed that with the following little tweaks:

• DO A BACKUP!!! In TWRP or if you use multirom, create a copy of your system and try upgrading that one!
• uninstall all patches and patchmanager
• uninstall aliendalvik-control (Actually, somehow I had two versions installed. The first one was removed fine with pkcon, but the second one has dropped an error. Finally, I removed that with this command: 'rpm -e --noscripts aliendalvik-control')
• disable to start android support at the boot!
• disable all openrepos
• disable all adaptation-community-<something> repos
• add/enable the following 2 repos:
  
  Code:

  ssu ar adaptation-community-common-hammerhead http://repo.merproject.org/obs/nemo:/testing:/hw:/common/sailfishos_3.4.0.24/
  
  ssu ar adaptation-community-hammerhead http://repo.merproject.org/obs/home:/mautz:/cm12.1/sailfishos_3.4.0.24_latest_armv7hl/

Some benefits of upgrading to 3.4:

• newer and much better browser engine
• camera viewer works again
• user 'nemo' will remain, so AD works without any further tweaking

It hit my eyes: "disable to start android support at the boot"
Is there a working Alien Dalvik for SFOS 3.4.0.24 on CM12.1?
Where? How? Advice please!

I'll work on 4.0.1.48 for hammerhead once that version works fine on my Note 4 (treltexx). (Hopefully soon.)
AD? Take a look at the other topic here.