pipes, you want some low end pipes like pro circuits, fmf gnarlys, paul turner mids, etc.
engine- you want good low end so you should get a mx port for your cylinders, a adjustable timing plate with +4 timing and thats pretty much it for motor.
wheels- you want to get 20 or 19" front and 18 or 19" rear mx tires. some examples are holeshot mxr4, mxr6 razrmx's etc. and you could get them on just .160 rims or .190 for extra strength.
suspension- you want some aftermarket a-arms and shocks. i run wicked 2+1 a-arms. if your doing strictly mx and wide open trails you should get 3+1 a-arms. you should then get shocks like works, tcs, elka etc. also you should get a shorter swingarm for a smaller turning radius like a -1 or a -2. then you could revalve your rear shock and get it done from companys like pro pilot, tcs, works etc. or you can just get a brand new rear shock for almost $1000! hope this helped.