Chris,
My car has an EEC-IV (Ford) management system, so I have some experience along these lines although it is not OBD-II. As mentioned, as long as the EMS you use was designed for a standard transmission, there should be no issue, BUT you will still need to provide load/no load inputs to the computer. I used a pressure switch on the clutch and fabricated position sensensing switch that is closed when the transaxle is in neutral. These inputs are in OR logic so that if either is "on", the computer knows there is no load on the engine (I am sure you will find that this is universally required.) In terms of the engine itself, you will have to implement the sensors required in one way or another if you plan to have the car's emissions checked by an OBD-II based test system. In the case of NC, custom/homebuilt cars are exempted from emissions testing. However, the only things that I did not implement were the airpumps and, of course, the catalytic converts (to which the airpumps connect.) The purge solenoid and charcoal canister for the tank vent were not difficult with my system. My point is that, even if it's not required, you can still make your drive train as clean as possible.
You will have to do quite a bit of research and study to either marry your chassis harness to the factory engine/computer harness or build your own harness from scratch. I found it easier to do the former. (In doing so, I actually found an error in the Ford circuit diagrams for the WOT A/C cutoff.) The biggest issue you will have is physically fitting the various devices in an already cramped engine bay. You may want to see if Oregon will give you the option of actual emissions testing (sniffer) vs direct reading from the OBD-II EMS system. With some engines, I have been told that it is quite possible to achieve legal emissions levels without every single device that was on the original car if a little tweaking and programming is done. Remember that manufacturers are striving for fleet emissions numbers, as well as, individual model emissions, so sometimes devices are used to help this overall fleet rating and may not be required for the individual engine type.
What is absolutely maddening about all of this is that, often, if you use a '60s engine, on which emissions wasn't given a second thought, everyone is happy! That is totally stupid if the goal is really to clean up the air. To me it is far better to be cleaner (while maybe not exactly to current specs) than to just pollute at will. But, that's just me. The Aussies have very strict requiements in this area, so maybe some of our brethern from down under can help. (Bye the way, even California exempts the first 500 kit/custom cars to be registered each year. At least, I think that's the right number, but you get the point.)
Regards,
Lynn