I think I got it figured out now... I asked about this in my own thread with kinda got off-topic... I have yet to try this, but my Lv. 75 RAmar has the quests more or less done on VHard... it's just a matter of leveling up enough to not get the crap beat out of me in SoTH.
Personally I do Secret Delivery and Doc's Secret Plan before the others, so I can get the Doc to make me weapons. Anyway, you tell Sue your name in Osto's Research. Then in Unsealed Door you talk to Sue - don't forget her, she's easy to miss (she's south of the S-shaped room). Then go way back, talk to Bernie and say "sure" when he asks you to talk about Sue. This is where I've screwed up twice so far... this is important.
Unlock Waterfall Tears. You have to talk to Sue on Pioneer 2 until she leaves, and Bernie in the caves (he's easy to miss too as he's out of the way; look for his arrow in Caves 1). Next is Black Paper... talk to Sue again and ask her a question (does it matter which? I think I asked the second one) and then talk to her again and she leaves. You'll find Bernie right in your path on this quest, talk to him and he leaves.
I would play "Knowing One's Heart" as well because Bernie is in this quest if you did everything right. He just says something, I dunno if it makes any difference though. Same with Seek My Master. I think you've done everything right when you get the extra ending in Soul of Steel.
I think this is it - I'm trying desperately not to forget anything as I do these steps with my Lv. 59 HUmar (I don't want to lose a third chance).
Does anyone know where I can find the SoTH script? I really want to read it again but the script site I know of doesn't cover this quest...