All my planets are specialized.
Any planet with 4+ slots gets a shipyard.
Most planets with 3 slots get a shipyard.
I put in the research facilities before the shipyard. (If Research III available, shipyard goes in first.) Only one RD per system.
The other questions I'll answer this way:
Mins 80+ or Orgs 110+ or Rads 110+ ... dedicated resource facility
All resources 50+ ... candidate for Monolith
Resources 50 to 100 ... dedicated research fac. (Can be converted to resource fac. when research nears completion.)
Resources 50- ... Intel, storage, system facs, etc.
That's the plan, but it never quite works out that way. Sometimes you have an abundance of high yield organics planets. Naturally that will up the minimum for organics. The tactical situation may cause me to build shipyards early either to get the needed ships or simply use up excess resources by building ships. In fact the tactical situation may cause me to change everything!
A lot of things I didn't mention, but that's the basics.