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Hi so I have a 99 Civic that absolutely runs terrible. I have no idea what's wrong and I haven't really talked to anyone about it yet. It has the stock d16y8 engine in it with no modifications other than an AEM intake. Whenever I hit around 4500-5500 rpm (so about vtec), The engine loses almost all power and it revs incredibly high incredibly fast. The guy I bought the car from said the engine blew up but was completely rebuilt. I'm not sure if he had a crappy, mentally challenged mechanic do this and messed it up or something. Does anyone know what's causing this? After I turn the car off and let it sit for a few hours, it runs normally (which isn't much better. There's all sorts of backfires and crappy sounding sounds coming from what sounds like the headers or at least something close to the front of the car.) Is the timing possibly off? Is the air fuel off? Anyone have any ideas? Do I need to completely rebuild it or just swap it? Thanks for any input.

 
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If you use it compet with 350Z, Audi TT, I totally agree with you. But I can stand for any chanllge amount those "Street Cars"
I have exactly same expersise about my 97 coupe Ex. But my AEM intake was a 2000 civic intake (1.7L parts) cut into 2 pieces, and put a Spect(Not sure spell it right) head to completely fail me the California Smoke test. (but all other result pass)
The repair bill is $500, I purchased Best replacement parts and do the repair myself. And pass the test. It somewhere does overheat after motor reached some points. Which case the uncomfortble driving feeling as you had.
I did repairs:
2 times oil change in 1 week. (check leaking, loosed tube, pipe, broken or retire pipe)
2 transaction oil change in month.(check oil tank level, checking transmission master clutch,pull air out transmission bleeding system if you add oil yourselves),
spark plug, wires,(make sure wires on the distribute rotation before pull it off)
Fuse Box, relay replacement. (may not issue here, but really helps make sure everything working properly, a fuse tester always include if you buy package)
Timing belt, and other 3 belts along with water bump, replaced when replacing my transmission master clutch from mechanic which case my car running wired.