Yes, all the bases do have to be touched.
Rule 6.09 of the 2011 Official Baseball Rules begins, "The batter becomes a runner when-" and part (d) continues, stating, "A fair ball passes over a fence or into the stands at a distance from home base of 250 feet or more. Such hit entitles the batter to a home run when he shall have touched all bases legally."
But, no, Howard would not have do the touching himself.
Rule 5:10 (c)(1), in a section addressing time-outs, clearly grants an exception.
"If an accident to a runner is such as to prevent him from proceeding to a base to which he is entitled, as on a home run hit out of the playing field, or an award of one or more bases, a substitute runner shall be permitted to complete the play."
So manager Charlie Manuel could have used anybody off the bench - even a pitcher.
It's cut and dried, with no other wrinkles, said Major League Baseball spokesman Mike Teevan.