First of all, congrats!
I would personally leave the sub distance setting to 12ft. The distance measurement is actually very accurate (something like better than +/- 0.1 ft), and it's measuring electrical and physical delay as a sum. Therefore, it reads your filters/DSP to be about 7ms of delay, plus the 4 ft of distance.
For cabinet resonance, I am not as impressed as you, but who knows what is audible and what is not, I mean, with the results of the incredibly scientific knuckle rap test.
Personally, I find that my C60 can't handles a xover lower than 80, however, it is close to floor, so I don't know how much is boundary and how much is inability. OTOH, my room is significantly treated, including floor. I probably push my center more than many here, if only due to distance and space in a dedicated theater. That said, trust your ears. My T55s seem to handle 60hz just fine, however, just not my C60.
Enjoy.