Well, since I uploaded all the files from the new download, the required permission settings ideally would have been stated in the upgrade instruction file. Also, I wouldn't have picked out the need to omit of the jpegtran (still don't know why this is needed so perhaps you can let me know?) on the global settings page because the thumbnail rebuild process stopped at a .bmp file and then it says the file type isn't supported.
Also, the need to edit the upgrade.php to include $skip_exheader="yes"; should ideally be stated in the upgrade instruction, along with the need to copy the /data directory, ensuring the permission settings are correct.
I mean it may be obvious if one is fully versed with PHP, Linux, and the opeartion of Photopost but still I think it could have been better. The instruction manual for the upgrade side is pretty bad. But the support is world class.