I only noticed the connections were off when I hooked up some combinators to see the output -- didn't have to do that a lot since I played with your mod. :-)
Anyway, thanks for updating! You're right about the connection points, but it really looks much better now. It may be not perfect, but there's no real need to further tweak the settings. Unless you have too much time to spare, I'd say leave it as it is. :-)