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No I have only shifted it manually with it not running but I did have the plastic housing cover off so I could see the shift mech move and it moved far enough it should be engaged all the way. That was my first thought that the shift cable not moving the shifter far enough because it has always been a little hard to shift. The cable moved the arm as far as I could move it manually without the cable.
The reason I looked at the shim under the top cover while running it with the unit all the way down there was a grinding noise, when i took the top cover off there were 2 shims one thicker than the other, i took one shim(the thin one) out and placed the cover back in place holding it by hand and the out drive gear locked into gear for the first time after reinstalling. At that point I bolted every thing back together and still same problem.