So you used the same rear sets as mentioned in the How-To (1998-2002 Honda CBR929RR/RC51) and took off the plate with all the holes in it?
I understand what you mean about the actuation concerning the arms, but does this mean Dennis Kirk has both that point up and down as well as ones that point fore or aft?
No, I mean the rearsets must have arms in the right positions. A shift linkage arm pointing rearwards on the left rearset wil move up and down when you shift it. You must translate this up/down into left/right in order to move your stock shift rod. You need a rearset with an arm that points up or down so that when you shift it, it moves left/right.
And yes I did cut off the plates that hold the heal guards. This was because I moved the left bracket to the right side and the right to the left so that the foot pegs cotated up and not side to side. This wasn't crucial because I don't really need the pegs to hinge but it makes the sets cleaner to have the brackets cut off anyway.
I can't take a picture of the spacer tube because it is hidden but maybe I can draw you a picture.