I have a burnam oil fired boiler w/ 2 air handlers for both heating and cooling. I am adding a 3rd air handler it's the same as my others but newer and has a circuit board instead of selinoids and relays The air handler is a First Co model #36HBXB-HW, a TACO571-2 zone valve and a Robertshaw 9400 thermostat. I have the 110 volt line in through a switch with a receptacle for the condensat pump, and the thermostat wired in. How does the zone valve get connected? Thereare 2 orange wires on the air handler labeled motorized valve do they just get run to the zone valve?and is it OK to power a 3rd zone valve from the transformer on the boiler?

You need the total amp draw if all zones are open plus amp draw of boiler, to know if current transformer VA is big enough.

Yes going large on the transformers VA ratings a great thing and can't hurt, I like the cicuit breakers on the 75va models! Cool idea!
And circuit board vs electromechanical relays is no different as to control wiring, its compatible.