I am in the market for a used car and am running into a few snags.?

Well, for one the auto market is much more global. A lot of "American" cars are made in another country and of course a lot of "Japanese" cars are made here. And generally speaking quality has gotten much better over the last decade or two. For actual reliability data taken from car owners, this is a great resource: http://www.truedelta.com/ . Also look at the types of problems for what you're interested in.

In general, however, Toyota and Honda have maintained their record of exceptionally high reliability, but I don't think the gap is nearly as high as it once was and would not rule out Ford in particular. What I think is most important is how the car has been treated over its life. While Civics, for example, are very reliable, one that's been neglected and/or hack modified will not be. So you'll want to evaluate each car individually, inspect it, search for signs of how well or poorly it's been maintained, check records if possible and get a pre-purchase inspection as a final step.

As for specific recommendations, I can only tell you what I would pick. I personally like sporty, nimble, fun cars--especially with manual transmissions--but want something reliable and efficient for daily commutes. So based on what you listed I'd be mostly interested in the Civic and Focus (but would take a Mazda 3 over either). I'd be least interested in the Spark. But that's just me and what I look for in cars.

Toyota Corolla

Toyota Camry

Honda Civic

Honda Accord

Mazda 3

American cars still badly made. The Ford Focus Racked up the high Recall Notices of any other car made or sold in the USA. They may have finally fixed all the bad problems. Toyota and Honda are the best made cars in the world. The 2012 Toyota Corolla is the one I would choose. The Honda is too old.