Ben another method as you have said drill through both E string holes with the guide block, turn it over and place the bridge over the 2 holes to see how they line up. This should give you an idea how straight the guide is.
You could possibly drill about half the width of the body in depth from both sides of the other 4 strings and hope the holes line up. They can be reamed with up to about a 5mm drill to make sure the hole goes through. Be careful to only drill from each side about half depth, if that makes sense.
Check the ferrule diameter think they are about 6 or 7mm hole.
Also do a test drill of the ferrule seating hole and depth before you drill the ferrule holes.
I use a bit of electrical tape around the drill bit as a depth gauge