Indexing of the shell plate. This is what makes every thing run smooth. This is best done in a quiet area for your listening to clicks. The LNL-AP has 2 index paws, one for up, one for down stroke. You need to watch the shell plate too, while you do this. Make sure the shell plate is tight before you start.
With only the shell plate in place run the ram up slowly watching for the shell plate to jump. While running the ram up slowly without hesitating and listen for clicks. If you hear 2 clicks it indicates the indexing is off. You want to adj the right index paw in 1/8 turns increments out (CCW) if it's not going far enough and in (CW) if it's over shooting. You can normally see the shell plate jump if it's not right. If you can not hear the click place a couple of fingers from your left hand on the shell plate, you should be able to feel it. Too much pressure and you will dampen the action. Once the detents get close it will cause the shell plate to jump the remainder of the way. This can cause problem of shaking powder out on 9mm rounds if this is happening. Adjusting it so it moves into position smoothly, will minimize powder spills. If you over shoot on the travel the shell plate will jump backwards spilling powder too. Do the same for the down stroke. You only want to have 1 click up and down. This adjustment is covered in the manual.
Now some more detail adjustment for the primer feed system.
First make sure the primer guide rod is straight, particularly after the bend that goes up (vertical) to the plastic retainer. This section of the rod must be straight for primers to have the needed dwell time to feed reliability.
Make sure there is no debree in the base where the sled runs. This area collects brass and powder so keep it clean.
I found it best to remove the primer feed tube and outer protective shell when making this adjustment. This makes it easier to see movement of the sled. Once it is adjusted correctly, there will be NO movement in the vertical part of the rod. This is critical to have the needed dwell time for primer to drop into the sled. Do a quick check an see if you have movement. If not your good as it's going to be. If you do have movement it needs adjustment.
Now with ram all the way up use the top adj (plastic retainer) and center the sled by looking down through the primer base feed tube opening. Now move the ram down to just above the bend, (Don't get into the bend section). If the sled moved out of center you need to do some adjusting. If the sled moved in or out, try adjusting the upper adj so the sled stays centered for the vertical movement. If the sled moved toward the bend, move the upper adj toward the frame. Then move up and see if it moved off center again. Continue the process till it stays centered at top and bottom of this upper section of the rod. Now if it does not stay centered no matter what adjustment you do your rod may have been bent during shipping. If this is the case you will need to bend the rod. Move the upper adjustment to the center for a starting point. If the sled moves out (toward the back) while going up the vertical section the lower part needs to be pulled out (toward the back) ever so slightly, (1/16"). Then repeat the adjustment procedure till you get no movement for the vertical part of the rod.
Once this is dialed in, it will feed as fast as you can move the ram up and down. Makes no difference if you change sleds (Large/small) this adjustment does not change. If it does your not running vertical. If I recall one size is more sensitive than the other.
This procedure will correct most all primer pickup problems.
Now if primers are not aligning up for seating, check for debree. It only takes a small piece of brass sliver or powder to keep it from going fully forward. If it's hanging on the seater, you may be riding the main press lever. The spring that positions the ram at rest is around the brass spent primer tube. Also check the seater to make sure it's fully retracted. Spilled powder can keep this from fully retracting. The best way is to disassemble it for cleaning, and sometimes a blase of air will work once you push the seater plunger fully out.