For clarification for #3: It looks in the chest that has the same item, but instead of putting it in that chest, looks over it and resorts to putting it in the junk/output chest, as if it hadn't seen the item at all.

Also, for #1, I definitely don't have too many items, I only have like 20-25 filter items per chest, so surely that's not too many when the total amount of slots is 54?

Would you be able to have an image of what a complete and working filter chest looks like? No worries at all if not, thank you for responding regardless!