This is the measured summed driver response with basic crossover.

I've been considering what distance to measure the complete speaker from and reached the conclusion that it has to be from head height at my listening spot. This is the only way to take into account the various room effects.

As seen above, the best x-over points turned out to be 500Hz LR24dB/Oct for Bass to Mid and 4500Hz LR12dB/Oct for Mid to Twtr and the Twtr's weren't inverted, to avoid a big dip at the crossover region.
This was my first attempt at smoothing the response, which was measured from my listening position.
I took out the 35Hz spike on the right speaker, but from my listening spot the right speaker had a huge suck out at 55Hz. I boosted this region by +16dB, which is the maximum available but even after correction it wouldn't do any better than the -6dB as shown on the trace. The corner location and adjacent stair well just suck this frequency dry on the right speaker. Its quite a wide band, but not a problem on the left unit, which is in a more open position.
Hobson's Choice here I'm afraid.
This 35Hz spike, which I must of had in the past, had been masking the 55Hz suck out I was inevitably experiencing when this bass driver was used with my Analogue/Passive crossovers.
With a small DSP lift, the bass is otherwise flat down to 25Hz, which is nice and better than I expected.
The plot shows it, but I can hear the mid range prominence on the right speaker, so I will reduce the level 1 or 2dB to match the left. I will also remove the small high spots on each tweeter.

For reference, the dimensions of my speaker layout/listening spot are shown below.
I don't have the speakers quite on axis with my listening spot, but they are turned in by 12 degrees.

I've been listening to this set up for a few days now.
It's better than the standard NS-1000M (by quite a large margin) but the mid range still has the same weakness I have noticed on every version of the Yamaha speaker I have listened to. This is regardless of whether standard, re-capped or active, not just with mine, with many different sets. With the 3" Beryllium dome, the upper mids are fantastic, so trumpet and sax etc sound superb and the system images so, so well. The weakness for me is the lower mid range, it lacks warmth, piano lacks the right timber from the middle to the upper-lower part of the key board. This area is just not convincing to me. I am going to try some other mid range drivers to see if I can find something that meets my exacting requirements tonally. This project is after all, the search for a speaker set up I will happily live with, for a long time.