Assid,
The new unit is almost 3 times the money that the 1124 is and with it being used for ~100hz and down I think the sample rate of the 1124 is fine. Also, like the 990, its not available yet.. Besides, I always keep focused on more power and the extra cash could go into more watts!
As far as the Mic/Preamp goes its as follows:
1) Not any mic will do. It to has to have a very flat response curve or measurements will all be a lie. The EMC8000 is pretty flat to 20hz, and the calibration file that comes with RTA helps to make it more accurate. Unless you want to send it away for calibration, which will give you a very accurate data model which you can setup a really accurate calibration file for your mic only (unless you bump it or something, then send it away again..). Most people find the one in RTA sufficient.
2) Parts express or your local Music store will have XLR (Balanced) cables unless you are a cable freak. In which case you will need to spend at least $1000 bucks on a 3 ft cable..
3) You plug the Mic into the Preamp (or Mixer) with Phantom power, which in turn is plugged into a soundcard like the EMU440 I described above into the line input (not the mic input).
4)The FBD will be connected to the 990 sub out (LFE, XLR Balanced) output. The output of the FDB will be sent to whatever Subamp you have.
4) You will be displaying your frequency response on your PC using the RTA software as you adjust FBD to flatten and correct issues with your room for your Sub. (or any other speaker)
5) Your soundcard will be used to generate test tones, pink noise or a frequency sweep which is send into the 990 input and thru the FBD to the sub.
Since the FBD will have a perminent home between your 990 and the subamp, its a good idea to also connect the MIDI out of the FBD to your PC and suck out the settings into a file for safe keeping... Or use the software Dundas mentioned that has similar capabilities for the FBD, but I have not personally tried it yet.
Hope this helps..