Solution to acquiring raw materials... including stone.
In the beginning the production buildings to produce raw materials were rather handy. But in time these buildings become more and more inefficient as you advance in levels. When these buildings start asking for Liquid Petroleum Gas, they instantly become counter productive. If this is where you are at, stop upgrading them because they have become "Red Herrings." At this point they consume valuable resources in large quantities that are so desperately needed elsewhere.
I'm going to make a guess that you have overlooked the most reliable source for raw materials. The one hour destinations. Actually any material destination regardless of time, is better then production buildings.
I know that your about to tell me, that the output of these destinations are at best "weak." This is because you have overlooked these destinations as Viable.
About level 100, I caught on to this. I sent ships to these destinations constantly as a routine. Especially the Cave and Gulf. Each time one of these destinations is exhausted, it upgrades with better output. About level 300, I had both the Cave and Gulf fully upgraded. Aside from Wood, I never had a problem collecting resources. My shortage of wood was resolved when the 10 minute destination was converted to a one hour destination.
Every chance you get, send your biggest ships to stone destinations, and in time your stone shortage will be gone.