You will need to give a bit more info because both are available with several petrol engines in the UK so apart from not getting the diesel versions in the US I assume there are a couple of options.
The manual box in the Focus is a decent gearbox, long lived and easy to use, clutch is light.
Not sure what engines you get in the Focus in the US but there is a 1.6, 1.8 or 2.0 in the UK, 2.0 isn't much more powerful than the 1.8 so most go for the smaller engine for better economy.
Don't know anything about petrol Calibers.
If you are going to keep the car for a few years it may be better to go for the newer car as it will have a warranty etc. and has already lost a lot of value.
$10000 for a 2006 Focus? Sounds expensive if it is the earlier shape but not so bad if the newer model which is also the underpinnings of the S40, C30 and V50.
My own car is a Volvo V50 and I have had no issues with it.
In four years time the Caliber will have been on the road for four years, the Focus for 10.
Focus is a better car, I assume by wagon you mean estate, rather than five door hatchback?