It would appear that at least some disk maintenance/repair is in order, but as you'll see, it is basically "repairing" software, especially in light of the fact that you replaced the HD with a new SSD, and are still having issues. I'm going to also assume that you do not have any other, more robust tools like Disk Warrior and/or TechTool Pro. So, here are a couple of things you could try.
First of all, how did you get all the software from your old HD to the new SSD? Unless you did a re-installation of OS 10.9.5, I suspect you would not have a needed (and hidden) partition. Assuming that is the case, you will need to create the (invisible) Recovery HD partition on your SSD. There are a couple of ways to do that, but the easiest is to use the excellent free program (actually it's a script) entitled "Recovery Partition Creator". You can get it from the link at the top of this discussion page about the latest version (3.8)"
http://musings.silvertooth.us/2014/07/recovery-partition-creator-3-8/
However, to use it, you must have a copy of the "Install OS X Mavericks" file inside your Applications folder. If it is there, great, but make sure you have a copy of it somewhere else on your SSD. If you don't have, you can re-download it from the Apple Store, and that download will place it inside your Applications folder. Again, make a copy of it somewhere else Also, make sure that downloaded version is 10.9.5.
In any event, run the Recovery Partition Creator "program". Just make sure to point to that "Install OS X Mavericks" file inside your Applications folder. I can tell you from direct experience that software works flawlessly, as I had to do it twice (and I did it with Yosemite, and it works!).
Once that process completes, re-start your Mac, holding down the Option key. You should see (at least) two bootable partitions, the one your machine normally boots to, and the one for the Recovery HD partition. Double click on the one for the Recovery HD. What you'll eventually get a screen that has the bottom choice Disk Utility. Select that, and then both Verify and Repair Permissions on your SSD, and Verify and Repair Disk on your SSD. If you can, do both of those at the Volume and Partition levels. Hopefully, when repairing the disk, it will re-build the directory for you, as to me, that seems to be one of the possible causes of your issues. (Both Disk Warrior and TechTool Pro can do that).
Once that is complete, restart your Mac. Not sure how much that will help, but hopefully you'll see improvement. Whatever the case, download the excellent free disk maintenance/cleanup program called Onyx. You can download it from here:
http://www.macupdate.com/app/mac/11582/onyx
However, DON'T click the download button! You need the version for Mavericks (OS 10.9). If you look further down the page, you'll see the link for that. Install and run it. I again can tell from experience that Onyx is an excellent program! In fact, I depend on it (as I do TechTool Pro and SuperDuper!), and it has always, always worked well.
Hopefully, after doing all that, you'll see improvement.
Finally, you should really consider investing in either Disk Warrior or TechTool Pro. I actually have both of them, and am I glad I do. Also, if either you are not making backups, or are using Time Machine, I strongly suggest you start backing up using the free version of SuperDuper! (you can get it from here:
http://www.macupdate.com/app/mac/13803/superduper). One of its' main advantages (especially over Time Machine) is that it creates a bootable backup, which can really come in handy. (The paid version allows you to schedule incremental backups, and thus it would behave like Time Machine. I actually did eventually pay for it, but I don't use this feature, as I don't require it).
