This might be for the best. The way I see it, you're trying to do two wildly different things: craft an overarching story featuring your characters, and writing a story for every SCP in the database (I will ignore for the time being whether or not the latter is a feasible undertaking for a single person). Both of these are getting in the other's way, and I think it'd be best to divorce the two concepts entirely.
You can still do both of these things, and I'd be happy to read either one, but they are at odds with each other. Now, I would focus on their story first and foremost. If there are SCPs that are relevant to the overall story, theme, plot; sure, work them in there - it'd be more natural, and you can tick off a couple skips while you're at it.
As for the Every SCP venture; there's always other smaller stories - or even series - you could tie some together with (I'm a fan of the 'one-shot' myself, and have done a couple like that), provided these connections are thought about, and incorporated in a way which makes sense.
You're already kind of doing this, but the links have felt forced or underdeveloped thus far. You only need to be more mindful:
How does this anomaly/item/character relate to my plot?
How does it impact the narrative? Does the overall story progress? Is it a simple character/slice of life piece?
Does it's inclusion change the characters in any meaningful way? Do they learn anything about each other or themselves?
Does the interaction change how my audience feels about my characters?
And so on, and so on. Best of luck.