In most cases the alignment calculated everpano 3D is giving good result, nevertheless in some cases it fails. Those cases generally tend to be organic situations with no vertical / horizontal lines, or many round shapes.
There's a new tool work in progress that will allow make multiple lines and just calculate the best orientation, or even completely reset the values and just leave the original panorama.

That tool was already there in version 1.2 but it was only ready for mac and was only accepting 2 vertical lines, the new tool will be available for windows also, and a part from being more performant will allow as many lines as you want to define.

grid to keep original alignment

Pipeline for keep original alignment :

1. - rename the original panorama you want to fake alignment
2. - download the grid pano TIF or JPG
3. - rename the pano grid as the original pano
4. - Create a new project in everpano 3D
5. - Drag the grid panorama
6. - The panorama will get a no rotation value
7. - replace for the orignal images in both the project folder and source

Kind regards