First: Perl! Emacs! (If not, this will be senseless...)
Use a perl script to generate your pdf. Easier than a makefile, better than a punch in the face.
When running pdflatex, use the '-synctex=-1' option.
Then, at the end of the generate script, use SumatraPDF to view the file:
'"c:\\Program Files (x86)\\Emacs\\emacs-23.1\\bin\\emacsclientw.exe +%l %f"',
This is fantastic, as it will reopen the pdf where you last looked at it (which is what you probably want) and you get to clicky on bits of the file and get them come up in emacs (which is also what you want to do).