Looking at you graphs, it seems to me that your sub is at least 8 db too high. Remeasure with the sub turned down 8 db.
Those Persona 3 F speakers speakers, if these measurements from Sound and Vision are correct, are not exactly stellar performers.
From those curves I would try bringing the sub in at 120 Hz as well as turning it down. The speaker curves and sub curve would tend to produce the results you are getting. So I would run the fronts full range and bring in the sub at 120 Hz as well as reducing its output 8 db.
Subs too loud are a very common problem.
If I got those curves from a speaker I designed I would consider it an unfinished speaker and continue with design modifications.
Those curves are from the persona package. Your 3Fs are the purple curve.