You don't need to swap the whole harness out, no. You do need to do a bit of wiring and swap out your ECU, but you're gonna need to do that anyway if you plan on swapping motors. And you're right, intake/exhaust on a 5-speed car don't necessarily mean it's going to be fast, but it will be faster than the same car, automatic, with intake and exhaust.
If you have to swap an automatic B16 just to beat 5-speed single cams, then I'd say you're taking the "I'm gonna prove that automatics can be fast" mentality too far. Automatics can be fast, but Honda ones usually aren't. They're designed for economy, not speed. Plus, a Honda manual tranny can take a lot more abuse (i.e. power going through it) than a Honda slushbox can. That's why you rarely see turbo'd automatic Hondas, the transmissions breaks after you start putting a significant amount of power down.
It's up to you though, but that's my suggestion. Think of it this way... you drop that auto B16 in there and pull on some guys with 5-speed single-cams. You'll be satisfied with that for a while, but what happens when somebody with a manual tranny B-series swap leaves you in the dust. Then you're back to square one.