Apologies for the delay in response here guys as I am in Europe and there is obviously a time difference
Answering the question about windowing - an indoor measurement is not as clear as one taken anechoically and those sent by Bruce are rather like that although it is not bad by any means. My own measurements are crystal clear, a strong main impulse followed by a virtually flat line with four 'tiny' fading reflections. What you are supposed to do is window just before the first apparent reflection (26ms vs 26.2ms in my case). Larry has windowed at 24ms although I see a fairly strong reflection at 19.6ms so this will be included in the calibration
Regarding room correction - I may be lucky in that my music room has solid walls and floor and I am able to keep speakers and chair well away from walls using the so called 'golden formula'. Using two subs has also helped so that I need minimal room equalisation: max - 1.5dB at just 33.4hz & 36.7hz and further very slight equalisation below 219hz - bass is very tight, dynamic and uncoloured (much less eq than Larry has used in Bruces' room which is in a range of -3.7 to +4.1dB between 116hz and 1469hz)
As for time alignment - I originally used DEQXperts from the manufacturers in Australia and also the Netherlands. They taught me a lot but I was never told to use unequal timing for main speakers which is what Larry has done (6.60ms LH main speaker, 6.68ms RH). Maybe it's something to do with Bruces' room or he is seated off centre? In any case time alignment needs to be checked by ear and I align the matched peaks of the subs to the first rise of the main speakers rather than the first impulse peak as Larry has done. I have listened to both arrangements and in my setup aligning to the rise rather than peak gives a natural and seamless bass response where I can clearly hear each instrument individually and especially the realistic 'growl' of a bass guitar from within the lowest frequencies
And for Subs - yes it is good that they take over the lower frequencies so that all amps and driver sets have a narrower band to work with (ie cleaner, clearer), in my case at 100hz with a 48dB Linkwitz-Riley crossover. Larry has used 120hz, 24dB and Butterworth so this may be related to the combination of speakers and subs that Bruce uses. I found that my subs (Miller & Kreisel plus B&W) sound slightly unnatural if I crossover above 100hz and at below this, my Open Baffles lose some attack
I must admit that I spent many months experimenting, taking advice, re calibrating and listening before I arrived at the optimum for my system so it all depends on how much time each of you can put into this. A DEQXpert (or another user like me) in a remote location can advise but only YOU know what you are listening to
With that in mind, I will mail Bruce and look at his latest measurements as suggested. It's a shame that this forum does not permit embedded illustrations as I could explain this so much better by screenshots of our two setups
Here to help if I can....