As far as which hole to use for the top link on your tractor there are a couple of variables.
Read your manual for some idea of which to use.
Also "if" your tractor is equipped with draft control your manual will provide the information if one position is more sensitive for the draft control then the other. Most of the smaller draft control equipped tractors sense the pull on the top link bracket.
In the case of the ripper it may be flattening the shoe out at it's designed depth,
one way to check that is to back over a ditch or hole and lower the ripper down to the desired depth and view the angle of attack at that level.