YARM is installed but not working. The technology is not showing up. The monitor item isn't showing up in filters, or in FNEI search.

I can cheat to get the yarm-selector-tool item, but when I try to make a shortcut to it on my toolbar, the item vanishes. I can select some ore, and the blue patch spreads out giving the appearance that it is working, and it provides a text verification that it was a success ("Added site N744 with 12,923,524 Stiratite") but the GUI never appears, and again, the tool vanishes from my inventory.

YARM does show up in the Settings/Mod Settings interface.

I'm guessing another mod is somehow conflicting, but there is no indication of a conflict in the mod screen (nothing is red, everything loads without an error).

Not sure how to list all my mods, but in a nutshell I'm running:
Bob's Mods
Angel's Mods
Space Exploration
Alien Loot Economy
LTN
Optera
Picker

and a few trivial QOL mods.

Correction: The GUI is working, it was just minimized. My bad.

The issue with the research being missing is still happening, however. And I can only get the item by cheating, and it vanishes after being used.

NameLips, The mod has changed so there is no longer a tool. See the description for how to use it now. It should be accessible through the burger menu (3 vertical dots) on your toolbar at the bottom. Hope that helps