So I decided to upgrade to Windows 10 and so far I haven't encountered any problems except that PCIE Gen 3 is not enabled.  I had to force this with Windows 8.1, so does anyone have a clean way to force it in Windows 10? 
 
Side note: If you have a g-sync display and an SLI setup, Gen 2 will cripple your performance by a lot (30 percent for me) as opposed to having Gen 3 enabled.  I made a thread about this a while ago.  G-sync has a 3-5 percent hit with SLI even with Gen 3 enabled (tested by me and others on this thread, Nvidia seems to care less about fixing this). 

Enable it manually via regedit...
 
#1 Press windows key + r to bring up the run box.
 
#2 Type regedit and hit enter.

#3 Goto  HKEY_LOCAL_MACHINE/SYSTEM/CurrentControlSet/Control/Video 

#4 Identify the correct registry folders for each of graphics cards you have installed. There will be one associated folder for each card installed. To identify the correct folder for each card, you will need to review the names of each folder within the “HKEY_LOCAL_MACHINE/SYSTEM/CurrentControlSet/Control/Video” registry directory. The folder associated with a graphics card will have three or more subfolders (depending on how many PCI-E slots available on the motherboard). The values listed for each subfolder will be 0000, 0001, 0002, 0003, 0004, and Video. Review only the subfolders labeled as "0000". You will know you have selected the correct "0000" subfolder when you see a registry labeled “DriverDesc” with a value that matches the graphics card you have installed. 

#5 Right click on the folder labeled “0000”. Select “New”, then select “DWORD (32-bit) Value“, then enter “RMPcieLinkSpeed” for the name of the registry. 

#6 Right click the “RMPcieLinkSpeed” registry you just created, then select “Modify”, then enter “4” as the data value and verify that the “Hexadecimal” option is checked under “Base”, and then select “OK”. 

#7 Repeat steps 5 and 6 for each graphics card associated folder (named “0000”) 

#8 Once you have completed creating the RMPcieLinkSpeed registry for each card, close the Registry Editor window and restart your computer. 

#9 Once your system is back into operating system environment, run GPU-Z and verify that the “Graphics Bus interface” value shows PCI-E 3.0 for each card. 

Sajin
Enable it manually via regedit...
 
#1 Press windows key + r to bring up the run box.
 
#2 Type regedit and hit enter.

#3 Goto  HKEY_LOCAL_MACHINE/SYSTEM/CurrentControlSet/Control/Video 

#4 Identify the correct registry folders for each of graphics cards you have installed. There will be one associated folder for each card installed. To identify the correct folder for each card, you will need to review the names of each folder within the “HKEY_LOCAL_MACHINE/SYSTEM/CurrentControlSet/Control/Video” registry directory. The folder associated with a graphics card will have three or more subfolders (depending on how many PCI-E slots available on the motherboard). The values listed for each subfolder will be 0000, 0001, 0002, 0003, 0004, and Video. Review only the subfolders labeled as "0000". You will know you have selected the correct "0000" subfolder when you see a registry labeled “DriverDesc” with a value that matches the graphics card you have installed. 

#5 Right click on the folder labeled “0000”. Select “New”, then select “DWORD (32-bit) Value“, then enter “RMPcieLinkSpeed” for the name of the registry. 

#6 Right click the “RMPcieLinkSpeed” registry you just created, then select “Modify”, then enter “4” as the data value and verify that the “Hexadecimal” option is checked under “Base”, and then select “OK”. 

#7 Repeat steps 5 and 6 for each graphics card associated folder (named “0000”) 

#8 Once you have completed creating the RMPcieLinkSpeed registry for each card, close the Registry Editor window and restart your computer. 

#9 Once your system is back into operating system environment, run GPU-Z and verify that the “Graphics Bus interface” value shows PCI-E 3.0 for each card. 

Ah yes, I remember this method from Windows 8.1.  Don't you need to do this every time you update your drivers?  Also, I only came across one folder from step 4, instead of 2 (one for each card).  SLI is working for me and I remember doing this in Windows 8.1 with two different folders, one for each card.  Perhaps Windows 10 condenses them into one?

gridironcpj

Sajin
Enable it manually via regedit...
 
#1 Press windows key + r to bring up the run box.
 
#2 Type regedit and hit enter.

#3 Goto  HKEY_LOCAL_MACHINE/SYSTEM/CurrentControlSet/Control/Video 

#4 Identify the correct registry folders for each of graphics cards you have installed. There will be one associated folder for each card installed. To identify the correct folder for each card, you will need to review the names of each folder within the “HKEY_LOCAL_MACHINE/SYSTEM/CurrentControlSet/Control/Video” registry directory. The folder associated with a graphics card will have three or more subfolders (depending on how many PCI-E slots available on the motherboard). The values listed for each subfolder will be 0000, 0001, 0002, 0003, 0004, and Video. Review only the subfolders labeled as "0000". You will know you have selected the correct "0000" subfolder when you see a registry labeled “DriverDesc” with a value that matches the graphics card you have installed. 

#5 Right click on the folder labeled “0000”. Select “New”, then select “DWORD (32-bit) Value“, then enter “RMPcieLinkSpeed” for the name of the registry. 

#6 Right click the “RMPcieLinkSpeed” registry you just created, then select “Modify”, then enter “4” as the data value and verify that the “Hexadecimal” option is checked under “Base”, and then select “OK”. 

#7 Repeat steps 5 and 6 for each graphics card associated folder (named “0000”) 

#8 Once you have completed creating the RMPcieLinkSpeed registry for each card, close the Registry Editor window and restart your computer. 

#9 Once your system is back into operating system environment, run GPU-Z and verify that the “Graphics Bus interface” value shows PCI-E 3.0 for each card. 

Ah yes, I remember this method from Windows 8.1.  Don't you need to do this every time you update your drivers?  Also, I only came across one folder from step 4, instead of 2 (one for each card).  SLI is working for me and I remember doing this in Windows 8.1 with two different folders, one for each card.  Perhaps Windows 10 condenses them into one?

Yes, you will need to do it every time you update your drivers. Perhaps... only one way to find out.

Sajin

gridironcpj

Sajin
Enable it manually via regedit...
 
#1 Press windows key + r to bring up the run box.
 
#2 Type regedit and hit enter.

#3 Goto  HKEY_LOCAL_MACHINE/SYSTEM/CurrentControlSet/Control/Video 

#4 Identify the correct registry folders for each of graphics cards you have installed. There will be one associated folder for each card installed. To identify the correct folder for each card, you will need to review the names of each folder within the “HKEY_LOCAL_MACHINE/SYSTEM/CurrentControlSet/Control/Video” registry directory. The folder associated with a graphics card will have three or more subfolders (depending on how many PCI-E slots available on the motherboard). The values listed for each subfolder will be 0000, 0001, 0002, 0003, 0004, and Video. Review only the subfolders labeled as "0000". You will know you have selected the correct "0000" subfolder when you see a registry labeled “DriverDesc” with a value that matches the graphics card you have installed. 

#5 Right click on the folder labeled “0000”. Select “New”, then select “DWORD (32-bit) Value“, then enter “RMPcieLinkSpeed” for the name of the registry. 

#6 Right click the “RMPcieLinkSpeed” registry you just created, then select “Modify”, then enter “4” as the data value and verify that the “Hexadecimal” option is checked under “Base”, and then select “OK”. 

#7 Repeat steps 5 and 6 for each graphics card associated folder (named “0000”) 

#8 Once you have completed creating the RMPcieLinkSpeed registry for each card, close the Registry Editor window and restart your computer. 

#9 Once your system is back into operating system environment, run GPU-Z and verify that the “Graphics Bus interface” value shows PCI-E 3.0 for each card. 

Ah yes, I remember this method from Windows 8.1.  Don't you need to do this every time you update your drivers?  Also, I only came across one folder from step 4, instead of 2 (one for each card).  SLI is working for me and I remember doing this in Windows 8.1 with two different folders, one for each card.  Perhaps Windows 10 condenses them into one?

Yes, you will need to do it every time you update your drivers. Perhaps... only one way to find out.

The method was successful, but only for one graphics card.  The second is still under Gen 2.  It seems like Windows 10 doesn't recognize the second card under the registry. 

Search the registry for "NVIDIA GeForce GTX 980 TI" and add the "RMPcieLinkSpeed" to all folders that contain the "DriverDesc" entry.

I performed a clean install of the Nvidia drivers to see if that would cause the second card to appear in the registry.  This worked and now both cards have Gen 3 activated.  However, a clean install always turns SLI off, so was I supposed to have SLI off before attempting this?  If so, that may have been why I couldn't see the second card in the registry.  Thanks for the help!

gridironcpj
I performed a clean install of the Nvidia drivers to see if that would cause the second card to appear in the registry.  This worked and now both cards have Gen 3 activated.  However, a clean install always turns SLI off, so was I supposed to have SLI off before attempting this?  If so, that may have been why I couldn't see the second card in the registry.  Thanks for the help!

Yes, sli should have been disabled. No problem. 

This actually did the opposite of what I wanted and what you said Sajin. Adding RMPcieLinkSpeed with a hexidecimal value of 4 made my GPU run in PCIex16 1.1 mode.

jdcranke07
This actually did the opposite of what I wanted and what you said Sajin. Adding RMPcieLinkSpeed with a hexidecimal value of 4 made my GPU run in PCIex16 1.1 mode.

You can just run the patch as admin and it will work. I did it for my backup rig when it was my main and had a 3930K (with Windows 10 pro x64).
 
http://nvidia.custhelp.com/app/answers/detail/a_id/3135/session/L3RpbWUvMTM0MDIyMzU2OC9zaWQvaDEzbE45X2s=