Response to Michael's "Honest Question": In urban areas the waste is treated. I have no idea how or what mechanisms are used.
In rural areas, there is no central sewer system. Each home has a septic tank, which is sort of a natural treatment facility: waste goes in, water comes out. The water feeds down pipes to a "leach field" that will water the lawn.
If everything goes perfectly, the system should work fine for years if not decades.
However, often the amount of waste going in can overload the tanks capacity. Then you have to get someone to pump the tank empty.
In the semi-rural city where I live, a hurricane that hit a year ago knocked out power and one of the first problems was that the sewer pumping stations couldn't pump.
On to your list:
1) Power
Urban areas will be hard hit by any significant loss of power. And powerplants will be hard hit by nuclear war, even if they aren't the target. For instance, they are extensively computerized.
I would guess most US power plants use coal. I can't find numbers on that, but nuclear is comparatively rare and hydroelectric is regional (northeast and northwest, mostly).
Again guessing, but I doubt they maintain much fuel in reserve. Instead, they rely on railroads making constant deliveries (once a week at least).
2) Traffic
As we found out during the hurricane, and New York was reminded during the blackout, fuel delivery systems require power. You can't get gas from the gas station if the gas station has no power.
Now, in dire circumstances you can run a hose from a hand pump down the filler hole into the tanks, but ...
Most people do not have a generator or anything like one.
There are bridges absolutely everywhere, but most of them will hold up just fine for a few decades without maintenence. After all, most of them have already.
I imagine our gas and diesel locomotives are much like yours: computerized to the hilt. AFAIK, an EMP will kill any car made after 1972 (the advent of electronic ignition).
Canalization is the exception, not the rule in the US. The New York State Barge Canal runs from Albany, NY (a seaport believe it or not) to Buffalo, NY on Lake Erie. The Mississippi River has locks on it. There are others, but those are the main ones.
Without constant dredging, many of our ports will begin to fill with silt. Sandbars will quickly block some of them.
There are a few museum-peice steam locomotives still around. Better still, there are several dozen that are still in use, pulling trains of tourists or as "working museums".
"Several dozen" locomotives will not be nearly enough. Also, the traks are already in poor repair in many places, and if you think diesel locomotives are heavy then you need to weigh a big steam engine.
A Union Pacific 4-12-2 was around 355 metric tons!
3) Farming
The amount of surviving farmland is enormous. Much of the farmable land is not currently farmed, and while the portion turned into parking lots is going to be hard to reclaim, the part that is somebody's lawn will be easy to plant crops on.
Most farm equipment is non-electric. Every farm I've seen has a tractor-pulled manure spreader. Farms are also far more likely to have their own generators and fuel storage. Of course, that makes them great for looters.
I have read that virtuall all US crops use sterile varieties. This keeps the farmer coming back for seed next year. It also pretty well dooms us if distribution networks are shut down.
Livestock should be ok. But I don't know that much.
Ham smokes well. Don't know about beef.
4) Medicin
Most of the US pharmeceutical companies do their manufactuing in other places. Puerto Rico is popular.
I don't know of anyone who NEEDS antihisitmanes. Hay Fever ranges from mildly to incredably unpleasant, but is not dibilatating. Get over it.
Distribution of drugs will be no better than anything else: if the trucks start we'll do well, but if they don't we're screwed.
5) Vehicles
There are car building plants all over the US. Toyota has one in Kentucky, while Honda IIRC is in Tennasee. However, in the event of nuclear war I think a new car will be the least of anyone's wishes.
Similarly, there are car-part factories all over.
Building bigger things gets harder. I don't know how many shipyards capable of building small craft there might be, but there are only a few that can build really big stuff and they tend to be close to other things worth nuking. For instance: Groton, Connecticut is home to the only facility in the US that can build a double-hull tanker, and one of only 2 that can build nuclear submarines. It is also close enough to the major east coast submarine base to be a two-fer. Make it a big nuke and trown in the US Coast Guard Academy across the river.
Newport News Shipbuilding is, AFAIK, the only facility in the US that can build a Nimitz-class carrier. It is also the other place that can build nuclear subs. It is also close enough to ... the largest navy base in the world, Combat Air Command Headquarters (formerly Tactical Air Command Headquarters), the HQ for NATO in the US, the Atlantic Fleet HQ, NASA's wind tunnel, and CIA Headquarters that the odds of it not glowing in the dark are slim.
San Diego has a major shipyard, as well as the main west coast Navy base.
And so on.
6) Organisations
You view of US "Militias" is held by a lot of Americans, too. I am sure that some of these people are dedicated and responsable, but ones in front of the TV cameras tend to be paranoid loonies.
Idaho is a popular place to "Get away from it all". A big chunk of the population there moved there because they wanted a place to get away from the government, and preferably one far from nuclear targets. If the "Survivalists" try to take over an area for themselves, Idaho would most likely be it.
The main obstacle they will face is how little they have in common beyond not liking most people and believing the government has turned evil. I mean, right now there are racist groups and religious groups and everything else that all make good neighbors because they all want the government to leave them alone. However, philosophical differences may prevent their ever unifying to become a government.
Right now, they think "We hate the government". Post WWIII that could well become, "I'm none to fond of you guys, either." Soon the white-supremecists want to conquer new lands while the white-seperatists want to leave other folks alone and the ...
You get the picture.
Some of these groups might just turn out to be Democracy's best hope, though.
8) Churches
I'm not a Mormon but I do know that the use of force has been a very divisive issue for the church in the past. Some believe it is wrong to fight others over their beliefs, others say that attitude got Joseph Smith killed. I'm not sure, however, how that applies to other use of force. I don't know, for instance, about serving in the military.
Most of the Muslim population is black, and urban black at that. Most of the Muslim population is also, IIRC, members of the Nation of Islam, which is a particular variant of the Muslim faith. Militant and organized would be two words well applied to the Nation of Islam. Armed is another.
9) Them Indians
The Native Americans (American Aboriginal Peoples?) are not a unified group. The individual Nations are spread out geographically as well. For instance, Nearly every east coast state has a "reservation" or two.
Some, no doubt, would welcome the collapse of "the white man's ways" and the chance to return to "the old ways". Most, however, have been so thoroughly integrated into mainstream society that they'd starve with the rest of us. Many of the others would be surprised to find out how truly hard-to-kill a buffalo is.
I doubt they'd try to rise up and take over. Much more likely in my opinion is a "Stay the f**k off my land!" attitude. Of course, they might take the opportunity to move to better land than the cast-off scraps we made them live on.
10) Refining
Lots, a few, fewer still.
Worse, our refineries are decentralized. There is a major pipeline that runs up the east coast bringing oil from Texas to refineries. That pipeline needs electricity to run.
I imagine steel and coal are a little better off, but they depend entirely on railroads to supply them.
11) Tough questions
In the immediate aftermath of catastrophe, I think people will be far too busy saving themselves to worry about others. Many of the elderly and bed-ridden will die before anyone thinks to help them. Many of the others will be turned loose, either through intent or neglect, and will survive or not on their own. A group of survivors may try to keep "the crazy guy" alive, but if he cannot find such a group, or cannot socialize enough to be tolerable, he will have to fend for himself.
Criminals will be largely forgiven, provided they contrubute and behave.
At the individual level, either everybody is foreigners or nobody is. If you were here when the bombs dropped, you're in the same boat as the rest of us now. However, if you came over after, you had better be offering to help. Otherwise, quit eating my food, quit drinking my water, and quit breathing my air.
) or a dull farm-worker. And we have invaded/attacked/occupied the Poles so often that we are the bigger thread. 
