We are building a roughly 1300sqft addition and remodeling a significant interior area of our ~1700sqft 2-story home in southern California (zone 3b). 

I want to use this as an opportunity to ensure our HVAC equipment and ducting is properly sized for comfort not just for the addition, but for the existing space as well. The existing space has fairly poor airflow in a few rooms and I feel the equipment is oversized and the ducts are undersized.

I’m wrangling with a couple of interrelated quandaries:
1) Is my existing equipment sufficiently sized for the entire new space?
Ideally I would like to keep our existing equipment as A) it reduces costs and B) we just upgraded it 2 years ago. The HVAC contractor we used did not perform any kind of load calculation and simply replaced our old unit with an equivalent sized unit. They also used flex duct directly off the plenum, which I have since learned is a sure sign of a poor installation.

I have performed a load calculation myself and had two other HVAC contractors do the same and based on the raw BTU/CFM requirements it seems our equipment would just meet/slightly exceed demand, even including the almost doubled square footage. This almost seems too good to be true given we’re expanding the area by about 75%, but I believe the main issue here is ensuring proper duct sizing to allow the equipment to optimally function. Our equipment is variable speed (both compressor and air handler).

2) Should I go with zoning?
One contractor recommended using a single zone to avoid space constraints and mechanical complexity of dampers. This would be ideal, but I would be concerned of imbalances between cooling and heating times of the year.

The other contractor suggested separate zones for upstairs and downstairs as he felt the equipment would not be able to fully handle conditioning the entire home at the same time even if within the load calculation. This seems like an odd suggestion to me as long as the Manual J/S/D are followed correctly.

3) How do I handle poor air flow, primarily in rooms with no returns?
Most of the rooms with poor airflow are bedrooms far from the air handler. I believe the supply runs to these rooms are too small, plus without returns having the door closed chokes the airflow considerably. I do not want to undercut doors and adding dedicated returns is likely infeasible due to layout. One contractor I spoke with suggested adding a jump duct which would connect the room to open space where the existing return is located. This seems reasonable to me, but is unclear how well it works in practice.

I guess my ultimate questions are:
-What is the recommended configuration for heating/cooling a 2-story home (number of systems, number of zones, etc.)?
-Is it possible/reasonable to have a single zoned system heat/cool a 2-story home comfortably?
-How can I handle return airflow from bedrooms without returns?