Patrick,
I've found most of these on the many pages of the CJ3B Page. Mostly in the Tech section. You just have to poke around.
Here are the short answers.
1: Yes - the intake manifold vacuum port for vacuum tube from PCV at 14.
2. Coolant drain - where the petcock would be (one on the bottom of the radiator too).
3. Yes. Oil circulation up to head (see 9) via 1/4" tube.
4: Yes. Oil pressure gauge flex hose to tube.
5: Optional by-pass for coolant connects to plug on water pump directly below. Otherwise, a pipe plug to close the hole.
6: 45* bend elbow for heater hose (other hose goes up to back of head - see 12). Or yes, plug if no heater. Doesn't need to be brass.
7: Yes. Top radiator hose (that's the thermostat housing) the "return" back to the radiator.
8: Yes. Bottom radiator hose (inlet).
9: Yes. Where oil line from 3 connects
10: Needed for block manufacturing. Needs plug.
11: Yes. Needed for block manufacturing. Needs special plug with small hole drilled through square head for return spring.
12: No. For heater shut-off valve (where heater return hose is connected - see 6).
13: This is the temperature sending unit for temp gauge.
14: Yes. Connects to "T" fitting after PCV then around to 3.
Hopefully, those boxes contain the parts you're needing to add to the block.