Point #1

The way i used to achieve this:

var scripts = [];
function getScriptStream(dir) { // Find it as a gulp module or create it
  var devT = new Stream.Transform({objectMode: true});
  devT._transform = function(file, unused, done) {
    scripts.push(path.relative(dir, file.path));
    this.push(file);
    done();
  };
  return devT;
}

// Bower
gulp.task('build_bower', function() {
  var jsFilter = g.filter('**/*.js');
  var ngFilter = g.filter(['!**/angular.js', '!**/angular-mocks.js']);
  return g.bowerFiles({
    paths: {
      bowerDirectory: src.vendors
    },
    includeDev: !prod
  })
    .pipe(ngFilter)
    .pipe(jsFilter)
    .pipe(g.cond(prod, g.streamify(g.concat.bind(null, 'libs.js'))))
    .pipe(getScriptStream(src.html))
    .pipe(jsFilter.restore())
    .pipe(ngFilter.restore())
    .pipe(gulp.dest(build.vendors));
});

// JavaScript
gulp.task('build_js', function() {

  return gulp.src(src.js + '/**/*.js', {buffer: buffer})
    .pipe(g.streamify(g.jshint))
    .pipe(g.streamify(g.jshint.reporter.bind(null, 'default')))
    .pipe(g.cond(prod, g.streamify(g.concat.bind(null,'app.js'))))
    .pipe(g.cond(
      prod,
      g.streamify.bind(null, g.uglify),
      g.livereload.bind(null, server)
    ))
    .pipe(gulp.dest(build.js))
    .pipe(getScriptStream(build.html));
});

// HTML
gulp.task('build_html', ['build_bower', 'build_js', 'build_views',
    'build_templates'], function() {
  fs.writeFile('scripts.json', JSON.stringify(scripts));
  return gulp.src(src.html + '/index.html'  , {buffer: true})
    .pipe(g.replace(/(^\s+)<!-- SCRIPTS -->\r?\n/m, function($, $1) {
      return $ + scripts.map(function(script) {
        return $1 + '<script type="text/javascript" src="'+script+'"></script>';
      }).join('\n') + '\n';
    }))
    .pipe(gulp.dest(build.html));
});

It has the advantages of concatenating and minifying everything for production while include every files for testing purpose keeping error line numbers coherent.

Point 2

Copying files with gulp is just as simple as doing this:

gulp.src(path).pipe(gulp.dest(buildPath));

Bonus

I generally proceed to deployment by creating a "build" branch and just cloning her in the production server. I created buildbranch for that matter:

// Publish task
gulp.task('publish', function(cb) {
  buildBranch({
    branch: 'build',
    ignore: ['.git', '.token', 'www', 'node_modules']
  }, function(err) {
    if(err) {
      throw err;
    }
    cb();
  });
});