Manuals are the same price in the US as automatics (or are more expensive)

This is absolutely false. Not every car is offered with manual transmission, but cars that can be configured with both are almost always cheaper with a manual. I cannot recall every seeing a case where it was the more expensive option.

Manuals should be cheaper because they're cheaper for manufacturers to make. Unfortunately, in the US they've become a niche product that doesn't move very well, so you're going to get a lot more resistance on price when you're haggling with the dealer.

My girlfriend's car got stolen a few years back. When I asked the cop how much this happens locally he asked me what I drive, and when he found out my car had a manual transmission he laughed and said nobody would steal my car - the kinds of people who steal mass market cars don't know how to drive a manual any more.

An example: http://automobiles.honda.com/fit/

$800 more with automatic, about 5% of the cost of the car.

Manual transmissions are almost always a custom order. You can walk into any dealer and ask that $800 be knocked off and chances are you will get it. But this only applies to the cars on the lot, which are almost always automatic.

If you are lucky the dealer might have a cancelled order on the lot with a manual transmission.

That's the purchase price. In the US, the market for manual transmission cars is smaller and so unless you plan on driving it into the ground, that manual transmission could very well end up costing the same.

On top of that, automatic transmission cars are more fuel efficient, so the operating costs might be a wee bit lower.

It wasn't clear, but I was talking about the lower resale value of manual transmission cars.