Just got back from the Vietnam/Bali trip last week and it was phenomenal. As many had mentioned before, I found Vietnam to be amazing and Bali to be OK but wouldn't go out of my way to do it. Just too overrun with tourists. Did get to experience the earthquakes as we were having dinner in Ubud the evening the second quake with a 6.9 magnitude hit on Lombok. Pretty harmless for us but obviously has caused a lot of devastation on the northern part of that island.
For Hanoi to Halong Bay, just hire a driver from your hotel. It's relatively inexpensive and is easier than doing the bus. Like others have said, fly Vietnam Airlines from Hanoi to Hue. It's relatively cheap, and I think we did business class for about $100 more. That helps with check in and the security lines. Get a driver from Hue to Danang. I think ours was about $30. You can then fly back out of Danang to get to Hanoi.