OK to start I think the confusion is coming from the fact that you have an aftermarket upper cable there that does not have the wheel to adjust the trunnion. OMC cables had that for the remote and throttle cables. The adjustment wheel was used to fine tune the adjustment and take out the slack which might be possible with the aftermarket cable you have. If that blue piece that goes through the mount for the upper cable is threaded and can turn, you might be able to do the same thing with it, as you could with the OE cable wheel. The way it works on the OE cables, the part the wheel is mounted on, fits into that cable mount, and you can turn the wheel to move the cable in and out. I would think the maker of the aftermarket cable had to include this same feature.
Also the procedure or order of steps in doing this is as follows:
1) drive off you adjust the shift rod height. This is the basis for all the other adjustments being correct. Once right it does not change.
2) drive off you adjust the transom shift cable with the remote cable and throttle cables disconnected, using the bell crank holder and the special tool to set the length of the transom shift cable at the engine shifter bell crank.
3) now you're supposed to reinstall the drive, and make sure its in Neutral. Mark the cable where it slides into the casing with a sharpie. Now have someone spin the prop while you use the cable, to shift it into reverse. Mark that position on the cable. Then shift back to neutral. Now have someone spin the prop, and you use the cable to shift it to forward. Mark that position on the cable. The REV and FWD position marks should be equidistant from the Neutral mark on the cable. This tells you that you are getting equal throw in REV and FWD on each side of NEUTRAL. If not, then go back and re-do it.
4) Now and only now, do you adjust the remote and throttle cables....
If you verify the above with the remote cable disconnected, shift the drive back to NEUTRAL and with your remote shifter in neutral, adjust the remote cable on the engine bell crank so it has no tension on it. Then with your assistant to spin the prop, try shifting it as above to make sure you still get the same equal throw in each gear position. This is a short cut method that may not work, you may need to try to do it the way its described in Midnight Wolf's instructions. Or try to get an OE BRP remote cable. Might be a pain to snake it up to your control, but might make it easier.
Also keep in mind if your remote control is worn out with lost motion, you will never get it right. I still have my original OMC control but I have a Teleflex CH 1700 that I want to install when I get the patience to take off and repair the coaming panel on that side. I did the port side last summer (rotted wood inside) and it was a REAL PAIN.