It all depends. If you're determined to stay all motor with the D16Y7 you could spend a ton and never hit that. I think you are severely underestimating the cost of reaching that goal. A good exhaust will cost you $400-500, a good header will cost $250-$400, an intake can be about $100, an intake manifold would be about $250, etc. Those are just a couple things and the prices are just rough estimates, you can go higher or lower depending on what you get, but all of that stuff would only add up to about 20+hp if you're lucky. The horsepower gains that you see listed when you're looking at parts are totally fake, an intake won't give you 10hp, exhaust 10hp, etc. To hit that 200hp mark you'd need a lot more.
Why focus on a number like that? Just concentrate on making improvements and making the car more enjoyable to drive. If you really needed to hit 200hp your best bet would be to do a GSR or LS-VTEC swap with bolt-ons and a few other things. But even going that route you're probably talking $4,000 range or easily more when it's all said and done. 200hp in a Civic would actually be very, very fast. Probably a lot faster than you actually think and actually need. My advice to you would be to do things slowly and one at a time and see how you like them before you dump a ton of money on a project with unrealistic expectations. There's nothing wrong with what you have and you can't learn all of this stuff in a couple of weeks.
If I were you and had $1000 to spend on what I'm guessing is a stock Civic I'd probably get an intake first, then maybe a cat-back exhaust. Get a decent brand because the mufflers go bad really fast in the cheapo ones and sound like s**t. After that maybe some lowering springs and whatever else you choose.