The Arduino build process will compile all the core files, but the linker will only include functions that are called (directly or indirectly) from your sketch. So you should ignore the object files and just look at disassembly listing of the .elf file.
A good way to do that is to use avr-objdump.exe in the tools directory: ?\arduino-0018\hardware\tools\avr\bin. The –S option dumps source intermixed with with disassembly of all modules pulled in by the linker.
Try it with the blink.pde sketch – You should get a code size of just under 900 bytes with none of the unreferenced functions you mentioned.
BTW, push and pop are in the millis timer interrupt handler. Because the handler is initialized in the Arduino core startup code, this handler is included even if you don't use millis or delay.