Thanks for all the comments and encouragement. It goes a long way. [cl
Mac,
Sorry to hear about your challenges. I wish I were smart enough to give you some advice on measuring the force and direction of the misalignment once installed. It's hard to decipher without looking but unless your trans has internal issues, you're already aware that the whining you're hearing is most likely coming from some side-loading on the input shaft.
Not something you probably don't already know and slightly over simplified: Although they're directly inline, your transmission input and output shafts are two separate pieces with gears on them. There is another shaft alongside these two that also has gears on it that mesh with the input & output shaft gears. This shaft rotates counter to the main two shafts and is called - get this - the "countershaft".
Here's the problem, if you're side-loading the input shaft from even a little misalignment, it's gears are going to mesh too tightly with the countershaft (aka: insufficient backlash). Now you've got noise.
Remember, we're talking thousandths of an inch here so I would think the best way to correct it is either going to take some machining (surfacing) to square-up your existing bellhousing or get another.
Also, when I write "side loading", that reference is in relation to the axial rotation of the shaft, so it could be pressure improperly applied up, down, sideways, diagonal, etc,
' hope this helps.