Since you are using an older Sony ereader, then you can still use the older Reader Library software. Your best option might be to just go back to using that since you are familiar with it already. Not many people are happy with the reduced functionality of the new Reader software. Did you actually uninstall the old software already? It might still be on your computer and then you don't have to start over. The old and new software are two different programs and exist independently on your computer (rather than just being a newer version of the old program and overwriting it).
Unfortunately for me, the T1 and T2 do not work with the old software so I didn't have this option. Not being able to order books in collections anymore is the main reason why I abandoned the new Reader software and switched to calibre. I also had about 1000 books and dozens of collections. The calibre software can auto-download the metadata info for your books and sort them into ordered series for you so it might be faster than you think to switch. calibre can be a little overwhelming when you first use it because it is full of so many features. For example, I was able to customize it to do things such as automatically sort some of my collections by publication date and some by date read and others by series order.
Good luck with whatever you decide to do and Happy New Year!