1) Crossover theory states that you need to pick a crossover freq at least 1/2 octave (and some people believe a full octave) above the -3 dB point of the speakers. You need to do this so that the imposed roll of the crossover itself is not interferred with by the natural roll off of the speakers. (Otherwise, you would have a dip in the response as the speaker's response drops as the freq is lowered until the sub kicks in.) So for your speakers, it would be:

Main’s – 44hz => 60hz (probably close enough)
Center – 75hz => 100 Hz (probably close enough)
Surrounds (4) – 60hz => 90 Hz

(1/2 an octave is a 50% increase in freq. 44 => 44 + 44/2 => 66 Hz. A full octave is 44 * 2 = 88 Hz.)

4) Turns out that you don't have to do this. There is a 10 dB boost applied to the LFE signal for DD/DTS soundtracks, but it is all internal to the player and software. If you use Avia or VE or any other DD test disc, you'll get the right levels. Just do *not* use the internal sub test tone of the 2900 to set the analog output level. Just like the Pioneers, it's hosed.