Whoa! I think you may be analyzing a little TOO much. Have some fun and go shoot for a while!

1) I watch for damaged vanes myself. It sounds like you're a pretty consistent shooter, so my answer would be to check them yourself. Number all your arrows and as you shoot groups, watch for those that don't hit at the same point and remove them from your quiver. Therefore, you don't have to judge if one rippled vane is worse than another; just make sure they still group with the undamaged.

2) I see your thought process, but disagree. Spine and/or nocking point should be the only factors that contribute enough to produce vertical differences. Think about it: if you're grouping fletched and bare shafts as well as you say you are to that type distance, then your arrow spine is SUPERB, which means that the fletchings don't get flexed into a position that puts their surface perpendicular to the direction of flight. (In other words, your "parachutes" don't have a chance to fight much against forward velocity.) To say that you might have tuned to a "less than ideal energy transfer" is WAY overdoing it! There are thousands of professional archers that are out there shooting scores that would blow you out of the water, and I bet most of their spines are NOWHERE close to as good as yours.

3) It points to the left when? at full draw? before drawing with the arrow on the rest? My best guess is that the string on your bow sits slightly left-of-center, when you hold the bow TRULY square in front of you. THEN, when you rotate the bow in your hand to line up centershot (line the string up to split your rest/riser), you have to rotate the riser counter-clockwise to do so, and it makes your stabilizer APPEAR to be pointing left. Even if that's not the answer, I wouldn't worry about it.