I can't help with mini-tweaker, I never used it. I have heard people talk about it but that was before I starting any modding. I have always used S3D.
As for the conflicts, usually you know when something was working fine until you added another mod and suddenly things don't work right anymore. You could have conflict in there all the time but never know it until you use the item that has the conflict. So there is not real answer to that question. When something doesn't work it could be a conflict with something else or it could just be a mistake in the files.
Peabody
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