well, for engines, anything D series will bolt in without a mount kit. A ZC will work well, and your stock si trans will bolt in (but ive never heard of a 4speed manual si trans??) Your ecu will work with the engine and little to no wiring will be required. ZC longblocks go for cheap and make for a good swap.
As for exhuast, its kinda up in the air on what you want. a good header seem to be unanimous with DCsports, comptech, and a few others. stay away from the cheap crap in jcwhitney, like pacesetter. For my hatch, I'm considering tanabe, but probably only for the muffler, because tubing is pretty much tubing (assuming mandrel bends, not crushed) and that I can get locally and not pay shipping. for your exhaust, my suggestion is going for about 2.5-2.75 inch piping, to a high flow cat (landspeed racing or random) into your choice of header.
I'd suggest getting a baffle for your exhaust so your friend wont make fun of you having a lawnmower, but hey, its up to you.
As for other things, air intake everyone will tell you AEM CAI is best, but if you wanted to you could make your own (
http://www.teamdelsol.com/-howto-/-c...diycoldair.htm)
good choice on the car, there is a lot of potential with 4th gen hatches, which is why everyone wants one.
civic4g.com, another link