Getting frame rate drops? / lag in EVERYTHING I do, cant find the cause or fix to the problem. Need Help.

So for the past few months Ive been getting frame rate drops (not sure if correct term) in everything. Not just gaming, but browsing, watching videos, everything. When I edit in final cut pro and go for playback it tells me I have frame rate drops, and the music or clip will cut out for just a second or two several times within a ten second interval. When I play a game such as League of Legends or Minecraft the same thing happens, my FPS suddenly plummet and it freezes for just a second or two then resumes. When I watch clips or videos, the exact same thing, it freezes for 1/2 second to 2 seconds. I have awesome connection with my ISP so its not that. I have run every test I can think of, Ive de-fragged my HD, I track RAM, Disk etc.. and they all run fine according tivity monitor and other tests. I did Disk Speed tests, I cleaned out my entire mac of all files I didn't need, I did a "spring cleaning" I rebooted into safe mode and a bunch of other modes I cant name. Im not an expert or anything close to that when it comes to computers, so if someone can give me a solution that would be great.

Also I took it to the Apple store a few months ago to replace the motherboard because the USB ports weren't functioning. When I got it back now that i think about it, thats close to when this problem began. Also my Keyboard lights never work, since I got it back.

Anyways, I get lag in anything I do, even scrolling down sometimes. I also wonder if it could be a graphics card issue? Not sure. Would love feedback! Hopefully something other than "take it into the apple store" 🙂 Thanks!

Processor 2.4 GHz Intel Core i5

Memory 4 GB 1333 MHz DDR3

Graphics Intel HD Graphics 3000 384 MB

Software OS X 10.9.2 (13C64) (Haven't upgraded to Yosemite yet but the problem started before that came out)

Also one last thing of concern is the Data Read / Write under Disk on Activity Monitor

Data Read: 46.15 GB

Data Write: 44.19 GB

Data read / sec: 176 Kb - 1.35 Mb (They fluctuate often)

Data write / sec: 24 - 96.8 Kb (They fluctuate often)

Again not sure if that has anything to do with it, but it doesnt seem normal...