If the goal is to stay NA, then I'd say that the most essential things to make high power will be:
1) long-primary exhaust headers to prevent exhaust pulses from one rotor from increasing residual and hurting volumetric efficiency in the other rotor
2) RX-8 e-shaft and stat gears to safely run to 9000 RPM all day long. The RX-8 rotors would get you to 10:1 CR from 9.7 for the S5 NA, but that's probably not worth the extra expense/hassle to machine them for earlier-style apex seals to deal with the peripheral exhaust ports.
3) Slightly later intake closing on the secondary runners/ports, possibly a half-bridge for more ram-air effect at high speed, and slightly earlier exhaust opening for a stronger blow-down to help exhaust extraction since the pulse won't hurt the other rotor with long exhaust headers. Since this is still a 'vert, with the extra weight and top-down cruising criteria (ok, I'm kind-of assuming that last bit), I wouldn't increase the exhaust overlap much, if at all, so you don't have trouble at low speeds/low loads/idle.
If you're aiming for 200+ hp, I would say that the focus should be on high RPM air flow, as long as it isn't compromising the low-speed drivability. For that reason, I wouldn't touch the exhaust closing or intake opening port timings, and would probably do only minor porting to the intake manifold and throttle body. Of course, opening up the intake pre-throttle and the exhaust after the long-primary header. For this, the stock MAF and ECU may get you close, but would probably clip the high RPM power through the rev limiter, non-ideal spark map for the mods, and through the MAF topping out.
A MAP-based ECU like a Megasquirt would be better as it would remove the MAF's flapper and smaller diameter from the intake system, allowing it to be opened up further, and it would allow more aggressive AFR & spark timing. I'm a big fan of the megasquirt, but they certainly require a lot of electronic comprehension, learning, and some patience in dealing with an open-source community vs a customer-focused company, and they aren't for everyone.
Supporting mods like a good radiator, making sure all the plastics are in place for good oil cooler and radiator air flow, and a bigger fuel pump and injectors (S4 or S5 TII should be more than enough) would also be in the cards.
Now, whether all of this is worth it vs a turbo-swap to get similar power but more torque... well, its a project and many times the decisions are made by the head & the heart, not just what is logical or most cost-effective...