The auto will bolt up, but to my knowledge, your stuck with an LS automatic tranny. Supposevly there are B16A automatics in Japan, but I haven't seen one sucessfully swapped into a Civic yet. I know one guy who did an LS swap auto to auto and he had to replace the entire in-car harness with that from an Integra to make it run (it wasn't fun). Since your Civic is an EK ('96-'00) you probably wont' even have the option (the wiring harness is much different that the EG and DC chassis). As westcoaststyle posted above, you'd also be hard pressed to find a computer to run your new engine. Even a B16A/auto computer would have an 8000 rpm redline and hurt your performance.

Bottom line, if you want to stay an automatic, stick with your D-series engine. If you really want performance, a small turbo system or nitrous setup will help, but I'd say it's just a matter of time before the tranny goes boom. Consistant fluid changes and being careful to not overheat the thing will help but it's not designed to handle a lot of power. If you want to swap over to a manual, that's a different story and probably the best solution (that or selling your car and starting with a manual version) if performance is high on your list.

Oops, I just noticed you have an HX. I really wouldn't considering pushing a lot of power through a CVT tranny, it most likely just can't take it. You might consider a D16Y8 ('96-'00 EX engine) swap and use that automatic. I don't know what's involved with that swap specifically, but probably wouldn't be too bad. Get a much more efficent VTEC system and extra 12hp right out of the box, and far more potential but honestly, I'd consider starting with another base car.