Ok here we go:
B. ''Marksman is your top spec for PvE'' - MM is the best spec in ICC,because u stand still and spam steady/autos,till then survival with trap dancing(expl shot/expl trap/serpent(overall damage with noxious stings) or kshot(specific fights/bad warlocks,mages,frost dk's and raid).
D.''Builds'' - Survival till ICC and more specifically till u have 4 set T10.
E.''Priority List'' For Survival : Expl shot>Kshot(under 20%) ,Explosive trap>Serpent>Multi-shot(dont even bother using aimed before ICC)>Steady
For MM serpent>Chimera>Kshot for overall damage,or Kshot>serpent>Chimera for specific fights (Anub/Yogg 0/Putricide/Sindra).
F.Armor Pen : Till ICC is your 3rd best stats after agility and crit(tested with Rawr/Simcraft,no matter what spec are u playing.
In reality armor penetration becomes good after u have 50% armor penetration passively,remember its always base on THE CONTENT that u do.
If ure playing in a fresh server,dont bother using arm pen trinkets,their proc is useless and overrated.
G. Dropping Arcane Shot - Just play survival with expl trap glyph till ICC,or MM for specific fights that gives u damage modifier/crit modifier. In reality u should drop Arcane once u have 470 arm penetration passively,but since survival is better if u can use the trap well ... yeah.
I. Glyphs - FOR MM: 1.Serpent 2.Steady 3.YOUR CHOICE(chimera/hawk for overall damage,or Expl trap IF u can use on CD),kshot for specific fights.
For Survival : Expl trap,Expl Shot, Serpent/Kshot.
J. Stats
Agility is 2x times better than crit and armor pen for survival,and 2.5x better than attack power and haste for survival,then u switch to arm pen MM build.
K. BiS Gear List try to get the highest agility/crit/armor pen items
L. Gems - Agility or agility/crit(if the bonus is really good(6+ or more agility,orange usually)).
M. Professions - JC is the best by far / BS is the second best(stats wise,think about why LUL).
N. Macros - Kripp macros video from 2009.
Edit : GZ u become a better hunter.
Edit: If u want more info about anything u can ask here,thanks.