My guess is the files are in the wrong locationThere's nothing wrong with leaving them where they are, but the Makefile.PL needs to be able to find them.
Going through the Makefile.PL, it looks as though you can tell the Makefile.PL process most (if not all) of what it needs to know by setting environment variables - eg set the JS_INC environment variable to the location of the missing header (.h) files, and the JS_LIB environment variable to the location of the javascript library (.a) files.
Specifying INC and LIBS on the command line, as already mentioned by
Anonymous Monk, might also work - though I can't be sure that the Makefile.PL won't clobber information that's being passed along by that method.
Cheers,
Rob