Unfortunately your template doesn't seem to work for me without quite a few tweaks. I have Arduino 1.0. I've followed all the steps in your guide, but I firstly get an error in Step1.mk "Error: no application found". That's because in Step1.mk ARDUINO_APP = /Applications/Arduino23.app when it should be just Arduino.app.
Upon fixing that, I then get
Sometimes I get an error that the compiler can't locate "pins_arduino.h". Doing the following fixes both errors.
In Step1.mk, change
Fixed. Arduino.mk now points to Arduino.app.
Also, inside Arduino1.mk "APP_HEADER = WProgram.h" appears to be wrong, as Arduino 1.0 uses Arduino.h.
APPLICATION_PATH in the same file assumes the Arduino 1.0 is called "Arduino1.app" also.
Most people won't have a number in their Arduino app name, it'll just be the default Arduino.app.
Arduino.mk addresses Arduino.app.
Arduino1.mk and Arduino23.mk makefiles are supplied for convenience.
CORE_LIB_PATH should have a lower case "Arduino" in the path, as it's lower case in the filesystem (in Arduino 1.0 at least). Currently, this won't work on case sensitive filesystems. USER_LIB_PATH should have a lower case "libraries".
Fixed for SketchBook/Library or library.
Fixed for /Applications/Arduino.app/Contents/Resources/Java/hardware/arduino
By default, OS X is case insensitive.
If leaving the target on All, an error "/bin/sh: Builds/nil: No such file or directory" occurs. After using other targets, the Builds folder is created so the error goes away. A Builds folder should be in the file template.
main.cpp in the project template should be Arduino.h not WProgram.h. Same in the C++ and Library file templates.
Actually, the #include in main.cpp is used to activate code-sense.
Fixed in the Library file template.
I hope to release the updated version soon.
Thanks again for the detailed feed-back.
Feel free to explore Xcode 4.3-related issues!