Hey, no problem!
I've never looked seriously into sub enclosure design but I think it's reasonably straightforward using a set of parameters called Thiele-Small applied to a set of equations. Of course one could get pretty exotic in those designs too...such as finite element analysis on the enclosure in order to design the near perfect bracing for the enclosure. I'd think the best eclosure shape would be cylindrical, or spherical for a number of reasons. Just my intuition.
I came across an excel spreadsheet some time back,
very nicely done I might add, which would do these computations and estimate frequency/phase response. I'll see if I can find that again. I'm sure there is a lot of information available, but this spreadsheet seemed to be pro-quality.
As far as getting rid of rattles, that sounds like a trial and error process. You'd want to tune to different frequencies to find them all (in search of rattling surfaces which have different resonant frequencies).
I'm almost sure the sub in my house here (a SV Sounds 20-39 PC+) is a bandpass design. I can tune it by plugging one of 3 ports. I think it sounds incredible but they are my ears, and they are not perfect.
A couple things interesting about the human ear...which relates to subs, class D designs etc. You may already be aware of this.
It turns out our ears are pretty insensitive to harmonic distortion at low frequencies. This is perhaps one reason why a class D amplifier design is more practical when driving subs vs. the complete audio spectrum. Our ears are sensitive to other waveform "irregularities" at low frequencies and are insensitive to the same irregularities at higher frequencies.
Added:
Haven't found the spreadsheet. These looked pretty good though. I'm on a linux machine here so I can't run these executables so I've not checked them out but again, this guy looks to know what he's talking about.
http://www.audiogrid.com/audio/