I tapped a hole in my motor (to hold the valve cover) but I don't think the pre-existing hole was deep enough. Can you make a tapped hole deeper? As the drill bit for the pilot hole should fit right between the threads, this should work, correct? Or am I flirting with destroying the threads I created?
You can do this, but you could possibly run into two problems (as I see it):
First, what you said about destroying the threads you already created.
Second, you run the risk of running into an oil or water channel when doing this kind of drilling. I don't think there is a great risk of it in the head, but there is a risk to be aware of.
As an aside, can you shorten your original bolt and still have it hold enough to keep the valve cover on? This might be a better option, if it's viable.