When was SIP instituted? Because a couple of years ago on my mid-1012 MBP I downloaded an open source office suite. I can't remember now whose it was. After that my Mac went to a slow crawl. I still had AppleCare at the time and was told to download Malwarebytes. It found it immediately and tossed it. Whew! Everything sped up.
SIP was instituted in El Cap in Sept. 2015.
I'm confused, though, because your symptoms sound more the product of poorly written software than like any kind of malware I've ever heard of.
