I own a two family building with two 200 amp meters on the first floor. The inspector wants a disconnect for the second floor at the meters and in the 2nd floor unit. How do I do this?

Very simply, this would require a main disconnect to be installed just after the meter, and then a 4-wire feeder would be used to supply the secondary service panel in the apartment, which would be provided with a service disconnect breaker. A common solution is to use an SER style jacketed aluminum cable assembly.
Technically, the Code doesn't require the second main disconnect at the sub panel location in the apartment, unless specifically required by the Authority Having Jurisdiction.

 have a 200 amp service and am getting central AC installed which requires two 2-pole 15 amp breakers. Is there a benefit in installing a sub panel for the air conditioning instead?

That depends. Usually a sub panel is only necessary if the main panel is full, or if more than just a couple of circuits are needed at a distance away from the main panel.

Why would only half of my house have power?

This could be from either a loose circuit connection, a bad main breaker, or a problem out on the utility line. Using a simple two-lead circuit tester that can measure 240 volts, check the power across both terminals of the main breaker, on both sides. If you are reading 240 volts across the wires leading IN to the breaker, then the power on the utility side is OK. Next check the reading on the load side of the main breaker. If it reads 240 volts, then the main is OK; otherwise it may need to be replaced. Lastly, take a reading between every two adjacent breakers (on the same side of the bus). You should read 240 volts. If not, then there may be a problem with one of those two circuits.

You may be experiencing a problem on the utility lines leading into your house, or you might have a bad neutral or other loose connection inside your main service panel.
You can contact the utility company and they will usually send out a crew to look at the incoming lines. Most of the time, there's no charge to you for this.
If the problem is not with the outside lines, then you may need to contact a licensed electrician to investigate the problem further.

I have a 30 amp sub panel with no ground. Can I drive a ground rod? Should the new ground wire be bonded to the main panel ground at the entrance?

Sub panels normally do not have a separate ground rod if they are located in the same building. If it is in a separate building, you can install a supplemental ground rod, but the grounding conductor must still be connected to the ground bus in the main panel, and the neutral conductors of all the branch circuits must be kept separate from the grounding conductors.

I am bonding an already installed CSST gas line to my main electric panel. I assume I connect the #6 bare copper wire to the ground bar in the panel, not the neutral bar. Is this correct? Any other tips?

The size of the ground wire is based on the size of the service entrance conductors to the house. If you have a 100 amp service, then the #6 is fine; if it is larger (i.e. 200 amp) then you may need #4 copper or larger. Coated or bare wire types are both acceptable for use. Grounding should be done at the panel that has the neutral and grounds bonded together (such as a main service panel, as opposed to a sub panel).