If you are going to take the time to put in a KL series motor, take a look at the KL-ZE. This is a japanese spec motor rated at about 200HP. It is an awesome swap for an MX-3 V6. I'm sure the protege would still need some fabrications.
As for the rotary....Good Luck! The only cars i've seen rotarys easily retrofit into are older Datsuns and VW beetles that have been converted into dune buggies.