-Although, what about an aftermarket crank? not needed, the stocker is more than fine.
-Also, on the head work, what is the recommended brand? I know crower, s2, omni, bc, etc all make head components. it depends which motor you're using. if you have a sohc, then id go with crower or crane cams and the required valve springs/retainers. a good port job is also a very good idea, as the sohc heads dont flow that well.
-Is a pnp a good idea for this amount of power? yes
-Even though you are saying it's safe to run up to around 550 whp, does that mean that it will be strong enough and reliable enough (granted a good build and tune has been done) that I wont have to worry over a period of time, let's say over a year or two. i hate to break it to you, but if you think ANY 400 whp honda is going to be reliable, not matter how well built, your only fooling yourself. have you ever driven a 400 whp honda? hell, have you driven a 200 whp honda? i was making 210 whp and i must say, 210 whp is pretty god damned fast for a street car. you will not be able to put down 400 whp to the pavement on any sort of street tire. nor will you be able to run 400 whp every day, you'll need to run more like 200-250 daily and then run 400 at the track. making 400 whp on pump gas on a d16 will be nearly impossible unless you have someone like jeff evans do your tune. even then, thats still pushing it.
-What about the c/r? and how do you figure what you want? 9:1. its proven to be about the best.
-What about injectors, how is the best size for your given hp determined? 750's or so should get you to 450 whp or so
-Anything need to be touched with the IM? yes, a very short, fat runner manifold is pretty mandatory
-New fuel pump, fuel rail, of course too I guess. yes, walbro 255 is mandatory and an aftermarket rail are a good idea.
-I'm sure there is plenty of other things...
yes there are. you need to do a lot more research. you've budgeted 2000 bucks, you're gonna need at least twice that. you will need to build your tranny, at the very least you need a good lsd, which is around 1000 bucks, and a very strong clutch, something rated to around 400 ft/lbs of torque or more. your best option would be a tiliton or exedy twin disk, but those go for 1600 bucks. 400 whp is too much power for the street, and i dont think you realize just what 400 whp is. my guess is you havent driven any really fast, really well built hondas, because you seem to think that a huge hp number is all that matters. its not.