I've been able to get ENB v0.113, Helix's 3d stereo fix, SKSE and MSI afterburner all working properly together. If you notice any issues with this solution please leave replies here. I would like to put together a package to make this a bit easier if I am able to get permission from all mod authors but for now it's just this set of instructions.

ENB

• v0.113 using the injector version (http://enbdev.com/mod_tesskyrim_v0113.htm)
  
• Note: The wrapper version will run but won't work properly with helix (for example no sun rays and I believe an issue with distant land LOD)
  
• ForceFakeVideocard=true in enbseries.ini

  ForceFakeVideocard=true

• Modify enbinjector.ini to include skse (see how below [1])
  
• In SkyrimPrefs.ini set the following before running with the enb injector otherwise skyrim may reset some of your settings as it believes the video card changed

  sD3DDevice="ENB"

• Note: Not strictly necessary but I'm currently using a modified version of sharpshooter's enb settings, other enb profiles may work well too. Just be sure to change ForceFakeVideocard.

Helix

• Helix mod 3d fix from April 4 2012 (https://s3.amazonaws.com/-HeliX-/skyrim.3DVis.zip)
  
• With skyrim version 1.6 it's preferable to use an ini tweak to fix shadows in stereo 3d (see note [2] below)

Dorkirts Skybox Mesh mods

• Available from 3D Vision Complete Compatibility Project (http://skyrim.nexusmods.com/download/37478)
  
• Note: This is fixed in helix's mod through shaders but there's a compatibility issue with enb which is solved by using Dorkirts mesh fix

MSI afterburner (likely similar for evga precision but I have not tested that)

• Open RivaTuner by right clicking on "MSI On-Screen Display server" icon in the task bar
  
• Select TESV.exe (add it if it's not there already)
  
• Do NOT turn on "compatibility with modified Direct3D runtime libraries". You can verify this by clicking the wrench icon after selecting TESV.exe. Leave that off and instead follow the next step.
  
• Turn off "On-Screen Display Support" (logitech keyboard lcd screen display will still work if you have it, albeit without fps display but enb provides fps display anyway)
  
• Note: This was the case whether using the normal helix d3d9.dll or the evga compatibility dll.

To launch skyrim

• Run ENBInjector.exe
  
• Run skse_loader.exe

This gives us in 3d stereo:

• enb including:
  
  • sun rays
    
  • ssao
• shadow fix
  
• Helix water fix
  
• sky, stars, aurora fix
  
• skse and afterburner running

-------------------------------------------------------------------
[1] Adding skse to enbinjector.ini:
enbinjector.ini

[TARGETPROCESS]ProcessName0=SkyrimLauncher.exeProcessName1=skse_loader.exeProcessName2=tesv.exe

-------------------------------------------------------------------
[2] Shadow fix with Skyrim 1.6
SkyrimPrefs.ini

bDeferredShadows=0

• This will use the old shadow rendering method. Helix's fix was great but it does not work with new worldspaces added by mods (and it missed a few vanilla areas as well)
  
• You should then be able to then remove helix's shadow fix by removing these three files from ShaderOverride\PixelShaders\

0DD4E031.txt
54548D09.txt
F25ADF18.txt