I think the Manual D does ductwork design, with the Manual J doing the heat load calculation.
You might almost do well hiring an HVAC consultant, a member of ASHRAE. He'd write a prescription for your house and then you could get at least five bids from HVAC contractors for each to bid on the same job.
Opinions are divided whether to tell each bidder that you are getting other bids. If I do tell a bidder and the smile disappears from his/her face I disqualify that bidder.
The contract should probably specify the max temp differences from room to room and the max air speed from the registers (to keep the noise down). Women are comfortable in different temps than men and this region of comfort is shown on some psychrometric charts.
I had a customer whose front door didn't close properly because the house had changed shape because of some flooding. I recommended she find a structural/civil engineer and then find companies who would do the work. They put some serious I beams in her basement for reinforcement and I'd think contractors would just have to guess at what was required.