Forgive me for jumping into this so late. You probably have moved on, however I wanted to add a few things to this discussion.
You may or may not already know that the aligner produces an edge that varies a degree or two along the length of the edge. This variance is different depending on the shape and length of your blade. I found out that if I clamp my Endura all the way at the base of the blade, then my angle is nearly the same, while if I clamped right at the center, then my angle changed by nearly two degrees from heel to tip. This effect would be much different on a knife whose blade width doesnt change along its length(and I would recommend clamping in the center in this case.)
With that said, you need to pay careful attention where you clamp your knife each sharpening session. I use a stone to scratch hash marks on either side of the clamp on the spine of the knife. Also, I'm not entirely convinced that the clamp matches angles on each side, so I would try to clamp with the thumb screw on the same side, say on the logo side. The thumbscrew also changes the angle, and I would tighten it down till it stops flush to ensure that you maintain the same angle from session to session. These steps will go far to reduce the amount of work you have to do each time you sharpen.
I have a ZDP and an S30v spyderco that I can get shaving sharp with the ex coarse stone. It's a gritty edge that scrapes the skin and kinda pulls the hair, but it will remove hair. I have been using my kit for about four years, and I still use a black marker two or three times each session. Mark the edge and work on it till there isn't any inkling of black left at the edge. Mark it again, and the black should disappear with just a few swipes. At this point, there should also be a burr along the entire length of the other side. Repeat on the other side, and there shoud be a burr on the first side.
Now you want to delicately remove the burr(with the same stone). Do this by alternately working each side with anywhere from five to twenty swipes per side(depending on the width of your bevel), and progressively get lighter each time you change sides. Be careful to maintain constant pressure each set of swipes, and be careful to get lighter each time you change sides. Do this about four or five sets of swipes, until you are just barely applying pressure(the lighter the better). It should also be noted that on this step, you should try swiping the entire length of your blade with one swipe. When you get to the lightest pressure possible, progressively lower the number of swipes per side(say 10,5,3,2,1). As an added measure, repeat the 2 swipes and the 1 swipe a few times to minimize any burr that may be there.
This step done properly should produce a nominally shaving sharp edge with the ex coarse stone. This will also be a mean slicing edge. After you get this result, you can move on to the next stone.
A quicker method of doing this is to produce the burr on the ex coarse and then move on to the next stone and produce a burr, but I prefer to get a premium edge with each stone before I move on to the next.
If you need to remove a lot of steel, there is an xx coarse stone available that fits the aligner. It is in the ski section on the DMT sight. It works beautifully.
One last note, I wouln't recomment using the aligner and the sharpmaker in conjunction with each other. You could use the aligner to rebevel, and then the sharpmaker to apply a higher microbevel, but you will have difficulty getting the angles to match from the aligner to the sharpmaker.
