The Si is WAY different than the EX. It's heavy as hell, so the boost in hp isn't quite as nice as you'd like to believe, and the styling is vastly different (many people consider 7th gen Sis to be ugly). Either way, this thread isn't about grilling him on his car choice, help him out.
Skip the chip - It's worthless at this point in time.
You need to decide exactly what you want from this car and how much you're willing to spend.
If you're just looking for a tiny bit more pep, intake, header, exhaust and done. It will not be a drastic change, but it'll give you a little more go.
For intake, I recommend going on ebay and finding the cheapest POS that'll fit your vehicle. If you want to feel better about yourself, you can buy a K&N filter and pop it on, but I really don't think the cost justifies the part. You'll gain very little from an intake, and it's not worth it to spend $250 for the slight possibility of half a horsepower more. I bought my intake for $30. I put some zipties around the couplers to ensure they stayed snug, and 7 years later it's still a done deal.
For header, do some research. When looking at reviews, you're looking for one thing in specific - make sure it doesn't crack. If you find one, and there are a lot of reviews about it cracking over time, move on. I'm personally sporting a DC header, but have a friend who has had a Megan on her Scion for years and hasn't had any problems. I spent the money on the "high quality" part, but I don't think it was worth it. I think you could be very satisfied grabbing a Megan, saving a few bucks, and calling it a day.
For exhaust, you can't choose an exhaust until you hear how it sounds. Look at a few exhausts that you think might be good and then youtube them for sound clips. Attempt to find sound clips from our generation of civics (01-05) as an exhaust system will sound different on different vehicles. Aside from this, you do not want anything larger than 2.5". 2.25" is supposed to be ideal, but most exhausts you'll find are 2.5". I personally went with the Skunk2
Megapower, and love it to this day.
If you're looking to spend a little more money, and want quite a bit more power, you need to look into turbocharging the civic. More time and effort will be required if you choose this path.