How to run HVAC supply /return & plumbing + keep out of the way
You don't mention which direction the floor trusses lay, but assuming they  run the narrow direction above they it will be a little challenging but hardly unusual. The best bet is to get your HVAC contractor and truss designer together to spec out openings in the trusses for at least the main supply and return trunks.  The truss designer is the expert, but I would expect the supply and returns to be separated by a few feet to avoid a large opening and a weak spot in the trusses.  The HVAC designer might prefer the trunks and opening be centered over the furnace, to make connecting the furnace easier and to avoid the plumbing under the main floor bathroom.  It means long runs to the foyer side of the house, but those are between trusses.

If you are seeking efficiency consider talking to a energy rater, specialist or Passiv house/efficient builder.   You have a nice small, simple structure.  With a modern tight (beyond code minimum) envelope and enough insulation you may be able to heat and cool with a few mini-split heat pump units instead of forced air.  The savings on ductwork alone will pay for a lot of energy improvements, and you'll save money and energy for the life of the home. There are plenty of resources, Greenbuildingadvisor.com, Building Science Corporation and the Energy Vanguard blog are some of my favorites.