Have you had a load calculation done? If not this would be the starting point.
What boiler are you planning on using? An oil fired hot water heater (ofwh) would be 80% efiecient and may be able to supply all your needs for a considerable savings of initial investment.
After the load calc you may find you need the 5 ton unit for the upstairs alone.
Variable speed motors are typically used to get extra effiency out of gas furnaces, seems a little overboard to me, a good system should be quiet anyway. You could have the system set up so the air handlers were 2 stage via blower speed in heat which would give quieter operation during much of the heat operation.