My Macbook Pro is freaking out at me, what did I do wrong?

I'm not quite sure when it happened, but recently my computer's software has become extremely glitchy, it all started at the same time. I will list off all problems:
1) F1, F2, F5, F6, F10, F11, F12 keys are not working. I've tried restarts, reboots, and safe mode. Nothing changed, except in safe mode. When in safe mode, my brightness keys (F1 and F2) are working fine, my keyboard brightness keys (F5 and F6) are still not working, and my volume keys (F10, F11, and F12) are responding, but when I hit any of them, it shows the volume at full like normal, except slightly gray, and with a small 'No symbol' or 'Universal no symbol' (the little circle with the diagonal line through it) on it.
2) Every once and a while, applications become no longer responsive for no apparent reason. This is usually Finder, which also makes it so my desktop shows the beach ball of death whenever I select it. In safe mode, I haven't had this happen. Yet.
3) You know how you can set it so your computer asks for your password when you open it after it's been on and closed for some time? Well, that's not happening even though it's set to happen. When I booted it up in safe mode, that seemed to fix the problem. Something else I might add, when I went in to activity monitor to see if anything wasn’t working (in normal boot mode, that is) I saw that ‘logicwindow’ was not responding. I did a bit of research, turns out that’s the thing that asks for your password on login.
4) The power button in the upper righthand corner of the keyboard part of my laptop isn’t working for turning the computer off (other than force shut down). If I go to the apple logo and click ‘Shut down’, ‘log out’, ‘restart’, or ‘sleep’, those aren’t working either. Just gives me the beach ball of death and then goes away. The 'About This Mac' option wasn't working in normal mode either, but it does in safe. I'm thinking the shutdown related things in that same section, but I don't want to try it now, due to the fact that Safe Mode is a pain to shut down and/or restart.
I’m thinking that these problems had to do with a program I installed a while ago called ‘CrystalClear Interface’. It’s one of those softwares that doesn’t show up in the applications folder, but does show up in that special section of System Preferences, where items like Adobe Flash Player and Java also show up.
Anyone know what the taco is happening? Thanks.

If this were happening to me, I'd get rid of CrystalClear Interface. I'd also try resetting NVRAM and PRAM. Also, maybe run EtreCheck, pasting the output here, so people here can see what it is you've done.

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My Macbook Pro is freaking out at me, what did I do wrong?

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