The only thing that confuses me at the moment is that the center point for the dimensions and the center of the motor shaft are not at the same point. I sent an email to my friend but I think he's traveling this week. I have noted both points on the attached drawing and it should be an easy matter to make that motor hole with sufficient clearance.
How did you determine "the center point for the dimensions"? I see the mark - red in the drawing and a yellow point in the annotations on the photo - and I understand that it is the reference point for all dimensions, but I don't understand how you chose it, or why you expect it to correspond to the shaft centre. Is it just a weighted average location of those bolt holes?
The bolt holes are not in a simple circle, and are generally offset toward the side of the transmission case which includes the differential and outputs - that makes structural sense. If you're looking at this motor as if it were mounted to the Toyota transmission - with everything centred in a line down the centre of the Supra - it would not be obvious why it is "lopsided", but remember that the case of this motor is designed for mounting transversely, with the transmission output offset to the rear of the motor (which is the right-hand side of the photo and drawings). It's not surprising that the fasteners are offset the same way. As a result, the adapter plate will stick out to the right side of the motor and Toyota transmission more than to the left side.
To me, it seems like all of the dimensions should be adjusted to use the shaft centre as the dimensional reference point: subtract 0.170" from all vertical dimensions and add 1.080" to all horizontal dimensions. That would likely make it easier when you get to the transmission side, since presumably all bellhousing dimensions will be defined relative to the transmission input shaft centre.