Cold air intake and full exhaust is ofcourse my first goal in the performance wishlist, just need to save up a bit.. Do you know approximately how much it will cost for each piece?
Depends where from, what brand, if it's custom, what your budget is etc it's a hard question to answer.
I mean for headers alone you can spend like $150 on some cheapy dc sports ebay headers, or all the way up to $1000 for a set of bisimoto's or toda's.

I'm not 100% sure about the vtec controllers purpose lol but i heard it controls where the vtec kicks in. It currently kicks in about 5500 rpm. When i redline (7450 rpm) and i change gears, the rpm drops to about 4600 rpm then it takes another 900 rpm for vtec to kick in again! Sorry if i didn't explain that properly but i hope you get me.
5500 seems a bit high for vtec on a h22a, don't quote me on this but thought it was meant to be 4800 rpm for h22a's, my old preludes was at 4800 and my civics at 4800 which has a h22a from a 5th gen type s prelude as well.
Maybe it's cause mine was the Type S model?
Regardless, it won't get any benefits without a proper tune/replacing some interals such as more aggro cams, all you'll do by changing the crossover point is stuff things up and probably lose power, the engines designed with a certain vtec engagement point which is based off the components and current tune of the engine such as the profile of the cams, the tune it is currently set to etc.

I like my clutch :P but im not sure what clutch it is, feels really good though.
Just cause it feels nice doesn't mean it's any good... often some heavy duty clutches make it feel like you're shifting gears in a bus, but at high RPM when shifting really fast makes it a hell of a lot better.

But i just dont get how it costs alot to remove a spoiler just because of them two holes.
You need to fill in the holes with putty, sand the bonnet back and respray it atleast 3-4 hours of labour right there. (That's if it's done properly)