OK one thing I did not see you do:
1) did you measure the shift rod height when the drive was off? If this is wrong, you will have problems, but once set right it does not change
2) you may be correct, there were 2 different design engine shifter bell cranks and that caused confusion. Look again at Midnight Wolf's instructions, I think he covers both styles.
3) if you totally disconnect the remote cable, can you shift it using that engine shifter bell crank (make sure you get a helper to spin the prop) from neutral to FWD and REV. Spinning the prop is necessary for the clutch dogs to line up. When you do this, will the load lever re-center with the ESA trigger lever? If not, then something is holding pressure against the transom shift cable. If the shift rod height adjustment on the drive was way off it could cause that.
What I did on mine:
1st set shift rod height when drive was off.
then did transom shift cable adjustment, then installed drive.
next used shift cable tool to adjust where the trunnion (mine was the adjustable kind) for the shift cable was the correct distance from the anchor point on the cable attachment point. I think it was like 6 1/2" but it was six years ago so I have to dig up the tool and measure.
Then with a helper to spin prop, used the transom shift cable (now just retained by the trunnion in the load lever, not hooked up yet to the bell crank on the engine) to shift from neutral to fwd and rev. I took a sharpie and made a mark on the cable where neutral, fwd and rev were and measured to make sure I got equal stroke on each side of neutral, very important. At the same time you helper can feel if its locking into each gear or not. Start with this and report back.