Brian
A very interesting mechanism and a lot of lessons learned. The problems with the connecting link reversing would have trapped me too and the simple solution of an elongated hole at one end is a good one to remember. The trouble that you had with the chain links jumping and the fix of moving the drive to the bottom shaft had me puzzled. I had to have an explanation for the improvement so I spent some time thinking. (what's that burning smell?) Here is my theory, others may think differently.
When you were driving the top sprocket, the top chain pulls tight and any slack in the chain causes the bottom side to droop away from the sprocket, reducing the effective number of sprocket teeth engaged allowing the chain to climb out.
When you drive the bottom sprocket, the bottom chain is pulled tight and the slack in the top chain droops to the inside of the loop, increasing the wrap on the the drive sprocket.
The key here is not the fact that one sprocket is higher than the other. The critical factor is that the droop in the chain must be on the top where it closes the loop and not on the bottom where it opens the loop.
If there are any different theories out there, speak up! I like to have a reason for things like this.
Jerry