Nice car. Your engine modifications definitely sound right on target. Since she's got an automatic, You might also consider an AEM (or other brand) adjustable cam gear. The EX engine has only one cam. Advancing the cam timing by 2 degrees (using the new cam gear), will shift the power curve toward the left. In other words you'll get a little more off the line punch, which could come in handy! The trade off, of course, is that you'll lose a little bit of hp over 6000 r/min. Of course, if your priority is maximum highway passing ability, then don't bother with the cam gear.

I have a 2000 Civic EX with OEM 15 inch Si wheels, OEM body kit, OEM Si mesh grille and H emblem, OEM Si 13 mm rear sway bar, along with an OEM Si leather wrapped steering wheel and shift knob, and the Si's chrome exhaust tip. All 100% genuine OEM Honda! The engine, intake, and exhaust are 100% stock, and I plan to keep it that way (as you can tell, I'm not a street racer). But I sure do enjoy watching other cars.

Maintenance is also very important, like you said. I follow my schedule to the dot, using nothing but genuine OEM Honda parts.

Good luck on your girlfriend's Civic. I'm sorry I couldn't be more helpful. Keep us posted as your project unfolds!