You can have a look at this, which should answer some of your questions re intake bellmouths and distances to airbox/airfilter.
http://www.bgideas.demon.co.uk/tmanual/Tm_Ch2.pdf
They give a rule of thumb that you should allow at least the bore diameter gap inbetween the end of the ram tube and the airbox (KN filter in your case).
There are also plenty of information and calculators available on the net about optimum runner length measured from valve to airbox (or air supply with assumed zero velocity).
Considering the importance placed in having a fully rounded bellmouth, I would assume that a filter sock over ram tubes would severly reduce the speed of the air coming around the bellmouth, negating any positive effect that it would provide. That said, we are probably talking 3/10s of FA noticeable change.
Keep reading if you feel like having a bit of a snooze:
An estimate of the first harmonic length for our L6s with a warm cam is somewhere around 3.3m, which is an aweful lot of runner. You can halve that figure to get the second harmonic length, and again for the third and so on. The gains from capturing that first pressure wave is estimated to be up to 10% gain, but diminish as you aim for the higher/shorter harmonics. Generally the 3rd and 4th are the only practical harmonics to be able to capture (about 0.8m & 0.4m, for about 4% and 1% estimated gain).
This is all estimated on the peak power rev range, so you can pretty much throw it all out and just go for the longers runner/airbox tubing that you can fit.
This site has some good reading and easy calcs http://v8soarer.com/intakerunners/index.shtml
Hope that helps.