I only just started reading this forum, sorry I'm late.
You said that you get some notes nice and bassy, and some just seem to disappear.
Then you said that you have "one AKG D-112 placed near the edge of the speaker cone... about an inch away ... Then I have a Rode NTK placed about two feet from the speaker."
I was thinking this could easily be explained by comb filtering. By placing one mic 2' behind the other, you've basically created a 2 millisecond delay. The result is a frequency response shaped somwhat like a comb (hence the name).
For more information on comb filters, see:
http://www.tcicomp.com/paul/dsp/chap4/
But then I started doing the math and it doesn't work out! You should be getting some peaks and cancellation, all right, but not at low frequencies. If I've got the right formula here, the nulls of a comb filter can be found by pi / T, 2 * pi / T, 3 * pi / T ... where T is the delay time in seconds. The peak frequencies are exactly half way between nulls, with the first peak being at 0 Hz (sort of like a low shelf EQ). With a 2-ms delay, that means your first null is at 1570 Hz, with the next peak at 2536 Hz.
So you should be getting some weird mid and treble coloration by combining the mics this way; but no serious low end problems except for a nice big bump in the overall low end.
So I thought I was going to give you the correct answer and now I've just convinced myself that I have no idea.
But of course, it's possible I've got the math wrong but the principle right. If so, you could find out by turning off one of the mics. If the problem goes away, then that's evidence that you're getting comb filtering.
Wish I had something more helpful to say...