that's a problem. you would need to be very clear why you want to go to grad school
My letters of rec are from professors where I have done well in their classes, but do not know on a personal level- they will be solid letters of rec, but not stellar.
these sound like generic letters
In general, MS has a higher acceptance rate because the student typically provides the money, as oppose to the professor or department. GPA is also less of a factor in MS. Usually, it's a cut off at 3.5 or above is good enough. Anything higher than that is mostly good for getting fellowships/grants, which saves the school money. 3.1 cum 3.3 core sounds like a question for your adviser.
Keep in mind that there are schools that almost never take MS applicants. For instance, U of M only accepted 1 MS (3% acceptance rate) last year. Terminal masters is not very beneficial to the school. It's the PhD's who make the huge contributions and really get work done for the university.