I found away around most of this. I wrote this simple .bat and it seems to open the files one right after another.
@echo off
start "" "X:\EXTRACTION\FALLOUT 76"
for %%a in (*.nif) do (nifskope.exe "%%a" )
return 1
As soon as I close the program it will load the next .NIF. I seen this was the fastest way to keep opening .NIF files automatically. As for the naming issue. What I did was went to my .NIF folder and did a CTR+ALT+RightMouseButton to "Copy as link". Then pasted that into notepad.
I opened the pasted .txt file in a spreadsheet to better organize the files. I chose the A-Z option and then saved the file. I used notepad to cut out everything but the file name and extension. Then renamed the extension to .OBJ since thats all Nifskope can export. So now when I click on my .bat file. All I have to do is copy the name and paste it on export. I found this to be the fastest way to tackle thousands of .NIF files at a time. Until someone can make something better this is the fastest way I found.

Nifskope Batching
https://drive.google.com/file/d/1tklpgw ... sp=sharing
I'm not very good at this writing scripts or .bat files but this does save me alot of time and hope it helps save time for someone else.