In the last two years I have been to every destination on your list (although not all the excursions/day tours) except Halong Bay and Phnom Penh.
I agree you are trying to do way too much on this trip. For comparison, I did just your Vietnam destinations on one trip (10 days), then Cambodia was a separate trip.
I think you need to pick what is really important to you and set other things aside for a future visit. For us (who also did this in November), Halong Bay was what we chose to jettison. Don't get me wrong, everyone should see it (I hear) and we plan to someday soon. But it was a case of "which of these is not like the other" in terms of geography and backtracking. It is a long trek out of your way from Hanoi to get over there. In the end we decided that spur and time it eats up was not worth it to us in possibly having to miss out on some other places. What pushed us over the edge was hearing that in November it can cold and wet there.
Other than that all the other destinations are definite musts; I think it's maybe some of the excursions you need to cut back on. We absolutely loved Hue and Hoi An. Hanoi and HCMC are also great to see but we thought the 2-3 days we spent in each was plenty (however, we did not go on any excursions, we simply enjoyed wandering the sights of both those cities without a specific agenda).
I have heard that Cu Cui Tunnels are not worth seeing unless you are a big Vietnam War buff (although I guess, is there such a thing?).
Amount in Siem Reap is perfect -- I would not cut there. They sell a three-day pass (that's what we did) and I would not have done it any other way.
Did I interpret correctly that you are looking at a package tour's itinerary and trying to re-use it for your own independent trip?
Do you already have hotels in mind? I have some good recommendations in these places.
SEA2BA