Well, if that is indeed not perpendicular, it is a non standard setup indeed!
1. First, do you have you dish rotation pivot at modified latitude angle of 40.35*, so modified elevation angle of 49.65* (says my calculator, for latitude 39.7*)?
Your photo WA0002.jpg would be about right, I guess.
2. Then turn your dish (with your actuator)
to such a position, that the distance from the rotation pivot to the middle left of the dish, is exactly the same as the distance from the rotation pivot to the middle right of the dish. This will be your dish-'perfectly'-aligned-to-pivot position, needed for due south aiming.
In your case it might be that your 'normal' top and bottom of the dish aren't perfectly vertical now, and the same goes for left and right not perfectly horizontal; but that is not really important. Important is the perfect aligning.
3. Now for setting declination angle: Use the
needed dish elevation for your fictive due south satellite position: 44.07* above the horizontal. Don't bother about the value of the (modified) declination angle in some manuals, though you can check that 49.65 - 44.07 = 5.59*
(yeah, a rounding difference), the needed modified declination angle.
You'll have to measure this 44.07 at the face of the dish, along the perfect vertical line; so you'll have to use a long flat piece of wood or so.
4. Do or check step 2 again, and then step 3 again. Due to the irregularities of your dish, you might need one or two repeats.
5. After you get these angles absolutely right, you can go finding your due south satellite, by turning the whole setup around the pole. Do you have a perfect south satellite?
Greetz,
A33