Let's try a different direction here. Your reaction sounds more like a software issue Vs a hardware issue.
Using your external keyboard & mouse locate the App ''Activity Monitor'' In the Utility folder. You want to launch it and then monitor CPU, Memory, Disk & Network keeping it on your desktop to the side so you can see it as you use your system.
* What you want to look for is to see if an app (process) is firing off in the same increment of time your mouse appears to get sluggish as you move it under CPU. Click on the headings to make the list easier to see.
* Look at the amount of memory being used are you getting high?
* Is there a pattern on disk activity when you are not doing anything
* Is there a high quantity of network activity when again you are not doing anything?
Let us know what you see.