I think I would take two bites at this particular problem.
First I would build a non isolated boost converter to convert the incoming 9v to 36v up to something just slightly above 36v.
Then I would build a full bridge that always runs at full maximum duty cycle through a transformer to generate the isolated 18 volts. As the primary voltage will always be up around 36v, the primary current will be acceptably low, and huge mosfets and heat sinks should not be required, efficiency of the second stage should be pretty good.
All the regulating would be done by the boost converter on the input side which will need to be built to handle high current, maybe 10 to 12 amps, but its only one mosfet.
Boost converters have a fairly constant input current, so should be the easiest topology to get through conducted emissions.
The four mosfets in the bridge can have their gates driven by a single transformer with four secondaries, because the duty cycle will always be a non varying 50% (less dead time).
The gate drive transformer could be driven by a flip flop such that the bridge runs at half the frequency of the boost stage and operates in phase.
The boost stage is pretty simple and can run just about any suitable PWM controller.
At least that is how I would probably do it...