Ok for those who might need to downgrade, this is what I did.
Since I've already set up categories, zones, taxes etc and didn't want to have to redo it, I went into phpmyadmin and exported database as text and copied and pasted it into notepad and saved to desktop.
Since alot of customizations were already done on the template, I also didn't want to have to redo it, so via ftp I downloaded my template files under includes/template/my template and saved it to desktop.
I then went into phpmyadmin and deleted all tables. I did not delete the database though, just left it empty.
I then logged into my server admin area and uninstalled zencart v1.5.0.
I downloaded v1.3.9, extracted and uploaded to server via ftp and then renamed includes/dist-configure.php and admin/includes/dist-configure.php to configure.php and changed the permissions on it to 777.
I also changed permissions on the following folders: (these two tips I got from http://www.kerrinhardy.com)
/cache
/images
/includes/languages/english/html_includes
/media
/pub
admin/backups
/admin/images/graphs
I then ran the Zen Installer in my browser and since the database and all file permissions were already set up beforehand, I had no problem with the manual install.
I logged into Zen Admin to check if all is ok and it was.
Next via ftp I uploaded the original copy of my template except for the includes/templates/my template since I made changes to the css and other files in that folder, so I needed to instead upload the files which I downloaded earlier, before I uninstalled zencart. So I then uploaded my modified template files into includes/templates/my template.
Next I opened up the sql text file I saved earlier in notepad and in phpmyadmin, I deleted everything in the sections where I have done modifications ie categories, zones, taxes etc. So after deleting everything under eg categories, I clicked on sql tab in phpmyadmin, then I looked for the corresponding data entries I saved in sql text file in notepad, I highlighted the relevant statements, copied and then pasted it into sql window in phpmyadmin, then click the go button. All queries were executed successfully. I did this one by one, for each section where I needed the info restored to what it was before the downgrade.
End result, it took a few minutes to do and I have the site up and running properly like it was before without having had to edit anything.
After that I just re-uploaded all the mods I had previously installed and everything is working perfect.