Installed clean install on new SSD and all my files showed up.

My mid 2009 Macbook Pro with Mavericks 10.9.5 has been running pretty slow so I installed a new SSD over the weekend. I made a bootable disk on a flash drive and was going to do a clean installation and restore my wanted files manually from my time machine backup.

When I went to do the OS installation an error came up saying something was wrong with my bootable disk. My next option was to restore everything from my time machine backup, which I did. However on startup after the installation the OS would just hang, usually with a blank desktop (no icons or dock).

I ended up putting my old hard drive back in, making a new bootable disk and then it allowed me to do a clean installation. Once everything was installed the system was up and running beautifully and surprisingly most of my apps and files were there waiting for me.

The system is working good so I'm not too worried but I'm just wondering what happened. I assume everything is there from my failed attempt to restore my time machine backup. How did that happen since I selected the install new OS on the when I booted off the disk? What's weird is that there are some tasks I entered just prior to taking taking out my old hard drive (they would have been backed up) that are there like they should be yet a handful of emails from years ago suddenly showed up in my inbox marked as unread. I'm also missing a selection of pictures in iPhoto.

Thanks for any thoughts!