What I mean is this e.g.:

You have a unique research for "stone-improvement", you have a unique building for using "stones" and then you get an abstract bonus like "construct buildings 20% faster"? That does not fit!

1) first of all all things that work together here should habe the same "level", so I would expect getting a stone-ressource out of such special buildings and research (that might be necessary for high-level buildings). If you look from the other side you could eliminate the special resreach and building for more general things that could be used for other ressources. A compromise could be that you add stones to the univeral material-ressource.

2)Stones and "constructing faster" doesn't fit. If you like to give a bonus it should be something like higher defense bonus to that (all) cities.