Need some help configuring my modpack

[DerpyGhost]

So over the last couple of days I have been working on a modpack and removing overlapping items and fixing issues with mod integration but recently I found some mods in my modpack that don't have options to remove their items in their configuration files and I don't know how to disable their items in any other way. How can I disable an item a mod adds without including an option to disable it in its config file.

For a clearer picture: In my modpack I have AE2, Buildcraft, and Thermal foundation; all three of which add a wooden gear and all three wooden gears have the same crafting recipe. I disabled buildcraft's gears but AE2 has no option to disable the wooden gear so I don't know what to do.

I also have Railcraft, Thermal Foundation, and Immersive Engineering and all three add "coal coke". I just want to keep the railcraft coal coke but don't know how to disable the other two since their config menus don't have the option.

Related: RFtools adds an aspect of dimension building which I don't want to include in my modpack, I want to disable the dimension builder item that it adds but it doesn't give me the option to do so in its config file, how do I go about doing this?