Almost able to have ENB v0.113, Helix's 3d stereo fix, SKSE and MSI afterburner all working properly together but not quite. Unfortunately when using the enb wrapper there are a few issues with enb like sunrays not working and distant land textures have an issue as well, but ssao and other enb shaders are working along with helix's water fix. When using enb injection you get enb sunrays and helix's shadow fix (no longer necessary) but helix's water fix no longer works.

Here's what I found:

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 [1] 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 injector 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" with helix mod. 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.

ENB method 1

• v0.113 using the injector version (http://enbdev.com/mod_tesskyrim_v0113.htm)
  
• Modify enbinjector.ini to include skse

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

• ForceFakeVideocard=true in enbseries.ini

  ForceFakeVideocard=true

• 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 water fix not working

To launch skyrm

• Run ENBInjector.exe
  
  
• Run skse_loader.exe

ENB method 2

• v0.113 using the wrapper version (http://enbdev.com/mod_tesskyrim_v0113.htm)
  
• Rename enb dll to d3d9_enb.dll
  
• Modify DX9Settings.ini to include

[General]ProxyLib = C:\Games\Steam\SteamApps\common\skyrim\d3d9_enb.dll

• ForceFakeVideocard=true in enbseries.ini

  ForceFakeVideocard=true

• 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.
  
• Some issues with enb such as sunrays and distant land textures

To launch skyrim: Run skse_loader.exe

ENB method 3
Tried using enb with helix as the proxy but this resulted in issues with both enb (no sunrays for example) and helix mod (no water fix).

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This gives us in 3d stereo:

• enb including:
  
  • ssao
• shadow fix
  
• sky, stars, aurora fix
  
• skse and afterburner running
  
• proper helix fix with water fix or proper enb including sunrays but not both

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[1] 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