Alienware 18 980m not detected

Most likely your secondary GPU fan won't be spinning because it has the wrong vBIOS. Each 980M has to has a different and specific vBIOS on the 18 for the fan control to work. I believe there is a vBIOS package for the 18 with 980M's on the Dell Support page. 

I'm not exactly sure why the 980M's aren't being recognised though. When you say that they also aren't recognised in the BIOS, what does it show? If it only shows the Intel GFX then the laptop is set to iGFX mode so the Nvidia cards are automatically disabled. This will happen when there are no dedicated cards in the laptop or when you use the Function button in Windows to swap GFX mode. 

Resetting the CMOS in the 17 and 18 is not as easy as the older laptops. You need to do an NVRAM reset. See link below. Just note that you do not need to remove the CMOS battery like it says in the post. 

https://www.dell.com/community/Alienware-General-Read-Only/Alienware-18-no-POST-How-to-reset-UEFI-BIOS-when-no-POST/td-p/5521711

When you install the 980M's and go into Windows, check the Device Manager. If the Intel 4600 graphics is shown under Display Adapters try doing the Function - GFX switch (can't remember if it's F5 or F7 on the 18). The Alienware OSD driver has to be installed to get the GFX switch to work. If it isn't, install it and try again. This should prompt a reboot to swap to the dedicated cards. If not, you could have an issue with one or both of the 980M's. 

The other option is to flash the unlocked system BIOS and set the video mode to PEG and force it to use the dedicated cards. Do this at your own risk. 

My Alienware 18 has almost the exact configuration as yours except that mine currently has dual GTX 780Ms in SLI, and it is at BIOS A13.

I have been researching how to upgrade to GTX 980Ms, and have discovered many requirements that apparently must be met.  'Requirements' include things like running Win10 in UEFI (BIOS) mode only, replacing MBR with GPT, and as MattB79 says above, flashing an Alienware 18 specific GTX 980M SLI VBIOS.

On the Dell Support page, under Knowledge Base, use the search box to search "Alienware 18 GTX 980M VBIOS"  The first entry should be: Alienware NVidia Graphic 980M VBIOS | Driver Details  Be warned though, that it says:  "for DELL service team use only."  I don't know how dangerous it would be to try to do it yourself, but I will be asking for software support when I get to that point.

Also, above you said that "If I place an old 765M in slot 1 and a 980M in slot 2, they are both recognized and work just fine."  My old school troubleshooting skills (I've been puttering with computers since the early 80's - TIs, 8088s, and 8086s, etc.) tell me that the 980M you did not use might just have gone bad, and when used with the other 980M, it might be disabling both now.

Another possibility is that IF the new cards have the correct VBIOS onboard (you didn't say where you sourced them from), then it's possible that you had them installed in the wrong slots the second time. (After installing the X brackets.)  The GTX 780s installed in my Alienware 18 actually have different part numbers, depending on what slot they are to be installed in.  (Possibly a master/slave, or primary/secondary relationship?)  You might even have two 'Primaries,' or two 'Secondaries.' -- Which if true, would then definitely require a VBIOS re-flash to correct.

I cannot say for certain without some actual "hands on" time, but maybe with a little luck, something I suggested may work for you.

Let me know how things go...  Everything you learn, helps me when I go to install my 980Ms.

Best of luck to you!