Learn English – Good expression for “things are starting to work”

Noting OP's comment that he doesn't want any suggestion of conspiracy or secrecy, I have to say I don't think there are many suitable idioms. OP himself says it's in the context of being more efficient - which I think implies the negative corrolary that involving management is less efficient.

The best I can come up with is Let's deal with this at the coalface, which I think emphasises the benefits of local autonomy without particularly maligning TPTB.

I guess you mean 'difficult to locate/find', rather than 'rare'. The commonest idiom for objects difficult to locate is needle in a haystack.

Red cars, for the man, were like needles in a haystack.

This means the man found red cars very difficult to spot.

There are several related idioms for things that are hard to chance upon. A couple of them (also mentioned here):

• scarce as hen's teeth
• black cat in a coal cellar