1.) Change your gay name
2.) wtf is a JDM bypass valve body? Sounds like turn signal fluid or something... A bypass valve integrates with your air intake for cruising through big puddles. Normally your car would suck in water, which doesn't compress like air does = engine go boom. Instead the bypass valve opens up above the water and sucks in air.
3.) There should only be one part to an intake manifold, unless you're thinking of the throttle body too
4.) The exhaust manifold bolts onto your engine, which should be 4-1 (or 4-2-1). Most JDM emf's are 4-1 though, leaving no "bottom part." If it's 4-2-1, then the 2-1 pipe connects to the 4-2 pipe. I'm a little confused what you're asking there.