Should have the AEPF, TXV and at minimum the Honywell VisionPro Thermostat for proper control.

AEPF426016C+TXV mated with the SSZ14042 is 15.0 SEER, 13.0 EER, 9.0 HSPF, ARI Ref # 1492630

Also, how did they come to the determination of the 3.5 ton sizing? Did they perform a proper Manual J heat loss/gain analysis?

not a fan of Goodman and especially not in a coastal location.

like Seaton mentions, I would get a load calculation performed for correct sizing.

IMO

They measured every room and window and added sun tracking and exposure and it was plotted on a computer program. They also read every vent and the return for air flow.

Should it be more or less then 3.5 tons?

Normally I would say 'less'. but it depends on the amount of insulation in the roof/walls and how many of what type windows.

Variable speed will help with humidity removal in your climate.

They did measure insulation, the great room has a cathederal ceiling with two skylights that I made storm units for and are fitted at the ceiling opening. There are not a lot of windows and they are old thermapane, 1983.

Sounds like the company did a very thorough analysis of your home and existing system/ductwork.