I'll second the heat check.  If your mini is like mine it doesn't take much
to push it up into the area of cpu throttling. This is a 2011 model and
currently I have it on a laptop cooler with the bottom of the case nudged
open.  Made a huge difference. Also installed fanspeed and adjusted
parameters so that  the fan ramps up earlier and harder.

Also, you mentioned using activity monitor to check cpu usage, have you
checked ram usage? Large amounts of swapping can cause beach ball behavior.
Look to see how may page ins have occurred as well as which processes are
eating the most mem. THough if no page-ins have occurred, swapping isn't
the problem. (page outs don't matter, that just indicates things being
shoved into memory)

Finally, yep, could be a drive flaking out. Which would be even more
obvious when combined with page-ins.
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