Okay, I am a bit unsure of the NSFW scene for Rune you want, but I presume the ending one. For that, yes, you need the crystal eye gem, go to lunch with Rune, and go to Rune’s class to fully start his route. Make sure to look at Rune’s mana balls in the morning first, (don’t whack him), so it will activate his lunch scene. In the baths, make sure to choose the “…jerked off to one of us here!” option in ‘Once Ago a Bad Boy…’ (never have I ever) for Rune’s path. Then keep going through the scene, and make sure you catch the crystal eye when Rune throws it to you! Keep going through Rune’s lore, and once back in the tower control room, you should be able to top/bottom with Rune, dependent on what you choose!
As for the bomb, as long as you input the right code, it should work! I’m still messing around, trying to find how to get Burry’s NSFW scene again, cause I haven’t seen it in almost 3 years… But to sum it up, as long as you do the option corresponding to the character, you should get their lore, path, and NSFW scene! I will get back to you for Burry’s asap! Also sorry for the wall of text, kinda hard to explain with so many intricate options!