This alignment is what I am talking about. You may want to re-do the stuffing tube. The last inch or so of the stuffing tube must be perpendicular to the motor mount, and pointed at the center of the motor mount. It does not appear that way in the photo.
When I set up a flex shaft, I like to be able to insert the shaft through the strut and stuffing tube and have it hit square on the end motor shaft. You should be able to put a short straightedge on the motor shaft and not see any deviation in the flex shaft, horizontally, or vertically. I know I have it right when I couple the shaft to the motor and the flex shaft exits the stuffing tube right in the center of the opening without contacting any edge of the stuffing tube.
Here are some examples. Sorry if they don't show enough, they are the best I have at the moment.
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