Yes, the goal is to use both of them.
The smaller board (P9X79WS) has been laying on stock for some time but I want to set up a second machine again.
One reason is also to figure out if the PLX chips cause more problems than benefit.
Since the boards are quite similar exept for the PLX feature I think I can make comparisons.

In the end I want to use both boards (and later an additional Z9PE-D8-WS) with boot options for nvme and multi-device use.

The easiest option for the P9X79E-WS would be to apply the bitfurcation setting on the sole PCIE×16@8 slot which is directly rooted to the CPU (Root Port 1).
This is a dedicated 8-lane slot which I imagine could be relatively easy switched to 4×4×, which would let me use 2 Devices on that port.

I would not touch the setting for the Root Port 3 at all, as this one provides the resources for the PCIE Slots #1 to #3 when #1 is the first slot below the CPU.
#1 and #2 are blocked by the graphics card anyway and #3 is provided by the same plx chip as #1 and #2.

If switching around on slot #4 (Root port 1) proves successful, I would try the same on root port 2 which provides resources for slots #5 - #7 on the second PLX chip.

This is what I believe to have figured out about the rooting: A bit confusing, but I didn't have the nerve to tidy up the image ;)



EDIT:
This diagram was provided by Asus and was shown on anandtech.com around the time the board was initially released:

Ohh, so no matter what, in the end you will want both modified, I gotcha now then! There is also lane reversal too, so you can switch things up (Adds to the pile)

OK, once you test the BIOS I provided, and we find out which of those works to show this BIOS section best, or if another edit is needed, once all is figured out I will do same edit on the other board.
Unless you want me to do that one now, and you figure out which method I need to use on it instead?

Yes, if you have the time, you could provide me with the same two mod versions for the P9X79-WS Bios (4901) and I'll see which board I can test first.

@paranoid_android - OK, I will do same change for now to the other BIOS. Whichever you test, only one needs tested for now, let me know which method works, or if both worked then I can fully complete the mod.
And, if both methods work, which method do you prefer (both, or switched)

Please give me the BIOS region dump from the other board
FPTw.exe -bios -d biosreg.bin

@Lost_N_BIOS :
Sorry for not responding for such a long time.
But I had to encounter several problems here... I had not set up a system on the second machine so I could provide the BIOS region dump that you requested.
While trying to set up a system, I found two of my designated drives reporting SMART errors and failing surface tests.
I had also tried (before the second drive failed) to set up win10 instead of win7 on the second machine which proved to be troublesome, as I could not find proper drivers for win10.
All of this together plus the pre-christmas hassle led to this delay.
As of now, I don't have a valid drive for the P9X79-WS machine to set up a system and to install Intel ME.
But I am currently working on a solution.
Thanks for your patience

Hey @paranoid_android - it's OK, we all get busy! On the "Second System" you can run FPT from DOS, just use the version from the DOS folder instead of Win/Win32 folder

SMART errors might be due to driver related issues, I saw Fernando mentioning this the other day I think.

Hi @Lost_N_BIOS - I have the Region Dump now.
This ist from the "Second System" - P9X79-WS with Bios 4901: Please note that the Bios is a modded one, with NVME Boot-Options added.

I finally managed to set up a system on a Sata SSD.
I used Win 10Pro because I hoped it would run a bit smoother with X79 chipset than win7.

But instead I seem to face new problems... There seem to be no updated drivers for chipset and onboard components for win 10.
Some are not recognized... Chipset drivers seem to be provided by microsoft or windows update.
But the Intel chipset Sata Controller is identified as "Standard AHCI Controller" while under win7 it was registered as "Intel C600/X79 AHCI Sata Controller".
I can't seem to get separate Intel Chipset drivers installed.
Nor do I find win10 drivers for some onboard components such as additional sata drivers.
Could I use Win7 driver packages instead?
Further, I cannot get the Intel RST drivers installed. Don't I need them for operation with win10?

Should I try to get a Win7 installed on the second system instead?

@paranoid_android - If you want I can do the NVME mod to the other BIOS too?

On win10 drivers, you should be able to install all from the below links, based on what each page says per your chipset. Install chipset first, that should update some of the items names
Intel Chipset Device "Drivers" (= INF files)
Recommended AHCI/RAID and NVMe Drivers
Intel RST/RSTe Drivers (newest: v17.0.0.1063/v5.5.0.1334 WHQL)
Intel Management Engine: Drivers, Firmware & System Tools
USB 3.0/3.1 Drivers (original and modded)

Or, on the Asus download page, choose Win8.1, all those drivers should work for Win10 too I think. If not, get ones you need at above links

As for moving forward with mods, I still need testing report from you on the other system, which BIOS mod worked (both or only one) and which method you preferred

@Lost_N_BIOS - Win10 has some chipset drivers installed wich seem to be provided by intel.
When I tried to install the INF-inst-utility (several versions), it either aborted due to compability issues or because the installed drivers were of newer date.
So I could not manually install AHCI drivers also.
I was able to install the Intel ME though.
But I will DL and try out the files that you posted.

Problem is, the system is now refusing to start up at all.
Recover and Repair Operations fail also.
I will try and setup win10 newly from scratch. But I find it strange that this quite new install failed to boot already.
I will have to do some validation of the installed memory and perhaps the CPU before a new install.

I will have to try out the mods you provided for my other system. Which is in fact my main machine, the one I'm using right now.
I wasn't sure if the system would start up after flashing the mod, so the other system (which now does not work) shoud have been my by-pass.

In general, I think its a good idea if you implemented the NVME mods to all bioses I provide also.
Could you rework the ones you sent me?

Plus, I did aquire an Asus Z9PE-D8 WS board. It is in mint condition, but in the end I would have nvme and bitfurcation mods applied on that platform too.

I'll have to do some testing and validation on both the current main machine and the designated "second" system.

Happy new year to you!

Hi @Lost_N_BIOS, I tried to write a modified bios (the switched option) using ftpw.exe.
I had copied the bin file into the app folder previously.

The operation failed, here is a dump of the command window:

D:\Tools\x86\Intel ME System Tools v8 r3\Flash Programming Tool\Windows>FPTw.exe -bios -f Switch.bin
 
Intel (R) Flash Programming Tool. Version:  8.1.60.1561
Copyright (c) 2007 - 2014, Intel Corporation. All rights reserved.
 
Platform: Intel(R) Patsburg Chipset - Reserved DID 0x1D41
Reading HSFSTS register... Flash Descriptor: Valid
 
    --- Flash Devices Found ---
    W25Q64BV    ID:0xEF4017    Size: 8192KB (65536Kb)
 
PDR Region does not exist.
GBE Region does not exist.
 
- Reading Flash [0x800000] 6656KB of 6656KB - 100% complete.
 
Error 7: Hardware sequencing failed. Make sure that you have access to target flash area!
Trying to erase the same block (iteration: 2)
 
Error 7: Hardware sequencing failed. Make sure that you have access to target flash area!
Trying to erase the same block (iteration: 3)
 
Error 7: Hardware sequencing failed. Make sure that you have access to target flash area!
Failed to erase this block 3 times!!
 

@Fernando - Microsoft doesn't stop Intel drivers from being installed, correct? I know Win10 is a pain in the xxxxxxxxxx but wow!

@paranoid_android - For the BIOS flashing tests, you have to flash via USB Flashback for mod BIOS on this board, sorry I didn't realize and mention that. And apologies for not noticing that back when I sent you the files.
Due to that, you'll need complete BIOS files not just BIOS region, here is new files to use, since you must do it this way. Rename the files to P9X79EWS.CAP as you test, each one must have this same name so only put on file on USB at a time.
http://s000.tinyupload.com/index.php?file_id=41473949488134764740 - Failed BIOS mod, do not use - final BIOS posted in post #74

Smaller the USB the better, format to FAT32 and put BIOS on root of USB. Yes, I remembered, NVME added to these BIOS

I'm not sure what's going on with your system that wont start, is that due to a BIOS I gave you?

@Lost_N_BIOS - Thanks, I had used Bios flashback method before on that second board to flash my own NVME modded Bios (4901+NVME for P9X79-WS).
That's the system that won't start. I reverted back to the official unmodded Version now, but at no effect.
Next I'll eihter try to set up win10 new from scratch or to run some memtests before that.
I am not really sure if it might be a hardware issue other than related to the bios or win10.

So I'll try to use your modified bios file(s) on my current system (P9X79E-WS) next.

By the way, this is my bios file I used for the system that won't start now, the P9X79-WS.
I used Fernando's modding guide to build it.

@Fernando - I am not sure either, only asking based of what paranoid_android said in post #24

@paranoid_android - that BIOS you attached looks OK. Does it boot to BIOS, and just not windows, or wont even boot to BIOS?