Tim, I also want to thank you for your efforts. All of this is already way over my head, and I would have no idea of what to do with the results once you're satisfied with the analysis - in other words how to use the results to design a better cross over.
Just a thought here - but at this point the question of interpreting the results is more general than the lead title of this thread "Question for Realistic Nova Experts"
Maybe starting a new thread with your posts #50 - #56 will get more of the speaker gurus involved in the discussion. I know double posts are frowned upon, but I'm thinking the analysis you're running is relevant to use of the software and microphone on any speaker, not just the Nova's.
Maybe a thread titled "Driver Analysis - Holmimpulse, UMM-6 Mic ?" will get more attention.
I took a simplistic look at the results (along the same lines as what you said in post #52) - we see that dip for both the woofer and tweeter(s) at around 1300Hz (? I can't see the scale very well, but the dip looks to be centered between 1K and 2K, but that scale is not linear (yes/no?). So I'm guessing those dips are around 1300Hz, which I had calculated, coincidentally, as the crossover point for the tweeters in the stock design.
So, did the original designers leave the woofer to run free as a cost savings measure, or for a sonic reason? They used electrolytic caps back then, couldn't have been much of a savings, maybe the inductors? Labor to install one additional inductor and a cap in Japan in the 1970's?
Does the software have modeling capability to calculate a response curve with different crossover designs once you have an accurate response curve for the drivers by themselves? If what you have so far is accurate, my guess is that moving the crossover up to about 2.0KHz on both the tweeters and woofer might flatten those blips out at 2.5KHz and add some protection to the tweeters. (another guess is that the original designers knew a hell-of-a-lot more about this than I do.)