I have a feeling this is part of a longer series, but I can't seem to find it, hoping you guys might remember it.
I know it was established spuffy, with Spike living at the house I believe. The part I really remember strongly was that Willow tried to intervene by using a spell that caused Spike excruciating pain in his bits if near Buffy.
I remember the spell hitting when Buffy & Spike were upstairs, and Xander & Giles tried to help. Xander was horrified by what was happening to Spike & Giles told Buffy to run. (To try and get as much distance between her and Spike so the spell wasn't as painful)
I do believe it got reversed quite quickly.
Does this sound familiar to anyone?

This happens in one of the stories of The Bittersweet Series by Herself. It must be one of the earlier stories but I don't know which one exactly.

flow

You're right flow it's 'What's It To Be' seventh installment of the Bittersweet series by Herself.

Summary: An ongoing series of Spike/Buffy tales, meant to be read in order.  The first springs from «Wrecked» in season six; the series veers off from canon at that point.  These stories are het NC-17, with some slashy flashbacks.  Winner of Best Series in the 2002 Watching You awards. Nominated in numerous categories in the Fall, 2003 Eternal Devotion Awards. Winner Best Conventional Pairing Series, Outstanding Conventional Author, Round 8 of the Shades of Grey Awards, November 2003.

Beware for those who don't know Herself's work, while incredibly beautiful, it's a lesson in Angst. The last story of this series left me, well... a bittersweet taste so to speak.

That series is on AO3, Sunnydale After Dark and Elysian Fields.