Hi Luis,
If you are modeling row-to-row shading of modules in the array, you don't need to use the 3D Shade Calculator. The shade calculator is intended to calculate shading loss data for arrays with shading by external objects like trees, nearby buildings, etc.
For row-to-row shading, called "self shading" in SAM you can choose the appropriate self shading option on the Shading and Layout page: "Standard (non-linear)" for modules with crystalline sillicon cells, or "Thin film (linear)" for modules with thin film cells. The shading options are described in the Help topic for the Shading and Layout page:
samrepo.nrelcloud.org/help/pv_shading.html
As for your questions:
1. The two plots on the Spatial tab of the results page for bifacial modules show the irradiance incident on the ground between rows of modules, and the irradiance incident on the rear of modules in the array. The y-axis for both graphs represents time starting with January 1 (Hour 0) at the top and ending with December 31 (Hour 8759) at the bottom. The x-axis represents the distance in the East-West direction (morning to evening) for one-axis tracking (assuming the tracking axis is defined by the azimuth angle), and from the front of the row for fixed arrays (assuming rows face the azimuth angle). For an azimuth of 180 degrees and one-axis tracking, the tracking axis is North-South so that modules rotate from East to West. For an azimuth of 180 degrees and fixed arrays (no tracking), the row bottom is the southern-most edge of the row.
2. The distance between rows is defined on the Shading and Layout page, and depends on the module dimensions, orientation (portrait or landscape), and number of modules along side and bottom of row. The "Row spacing estimate" on the Shading and Layout page is the distance between rows.
3. See my answer to #1 above.
4. For this analysis, I think you should enable self shading.
Best regards,
Paul.