Ok Im gonna summarise this stuff cos the post is just too long to respond to its going to take me ages but I'll try to summarise the main point.
As I said before the battle in origins is a point of reference that is the purpose of origins in this discussion as far as im concerned its PIS. You cant get as annoyed as much as you like but its my opinion and im going to give my reasons:
1) Cap is a smarter and better fighter
2) Cap is faster
As I have said before Cap is the leader of The Avengers Wolverine is not Wolverine takes orders from Cap when he leads superheroes into battle that includes the xmen (Secret Wars 1 and 2 probably). Wolverine would step up if he thought he was a better leader( becuase its a matter of life and death) and Cap would take orders.
Wolverine does not have intelligence showings of himself being able to get out of a device created by alien shapeshifters. Cap has with no powers.
Captain America in general shows himself to be more intelligent.
Cap is a better fighter and it is PIS that Cap has problems with ninjas because:
Daredevil is classed as Athletic
http://img218.imageshack.us/img218/7518/civilwarsfiles014sn7.jpg
Cap is classified as Enhanced Human.
http://img214.imageshack.us/img214/5494/civilwarsfiles011sc6.jpg
See what Shield have to say about Cap vs DD
http://img187.imageshack.us/my.php?image=ct2tb2.jpg
As you know DD beats up ninjas on a regular basis. If Cap can handle DD hes not having problems with ninjas.
I also said when Cap had problems with ninjas that was in WW2 wasnt it? Wolverine had to be better than Cap at some point, when I said Cap was doing something for a hundred years that is just figure of speech.
Wolverine can be a sloppy fighter sometimes. Cap is never a sloppy fighter. I dont always believe it because Wolverine can withstand damage its because he is just downright sloppy. Eventhough Wolverine beat The Wrecker he still allowed himself to be thrown, that is something Cap would never let happen. Cap could also survive this attack because he has jumped out of planes with a parachute....but he wouldnt let it happen. Then theres The Punisher hitting Wolverine in the nuts.
The problem is you know more about Wolverine than I do and sometimes you got to admit he can be a fool sometimes.
Wolverine is fast but at the end of the day he still doesnt have anything to match dodging lasers in zero gravity
Now the problem is wether Cap can knock Wolverine out. One thing I dont understand is that you said there were these people who could kill Wolverine with one touch, if these people can do that Cap should be able to do that. Cap is a master of all martial arts therefore he should know how to use chi. I know that chi is used in some of the martial arts he knows.
Also Wolverine is very inconsistent with his healing factor. One minute he is being taken down by a nut shot, then he isnt as for the Namor example it looked like Namor was standing inf front of him when he punched him but i'll check it out. To be quite honest im not sure what to say about his healing factor, but I still think Cap is faster and smarter.
PS. Checked out the scans yes it was to the back of the head.