Being a DIY speaker designer is hard and has a learning curve. Trying to do "timing" measurements in room is one of the hardest things. I recently went through this and used 6 different time alignment methods and got 6 different results. I definitely do not have all the answers but a few things to consider.Thanks for taking a look.
Can the delays not be estimated by viewing the overlayed Impulse response?
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I read elsewhere that the delays can be set by aligning the rise of the tweeter and mid with the woofer?
1. What Mic are you using? If a UMIK-1 it probably is not accurate enough for this type of work. A UMIK-2 or a "regular MIC" using a 2 channel interface so you can do loopback measurements will work. See link for REW designers comments https://www.avnirvana.com/threads/acoustic-phase-measurements.13300/post-99941
2. To align you need to do identical full range sweeps of the drivers without any filters. The REW alignment tool works well for this for the "mid" to "Tweeter" but woofer alignment is extremely difficult with "in-room" measurements no matter what anyone says. If possible timing measurements are best done "outside" in a large open space as far above the ground as possible but often this is not possible. If not I would try several different methods on the woofer (REW alignment tool, REW Wavelet tool, overlayed impulse method (the problem is what do you align? front? first crossing, peak, ?) , nearfield woofer and mid impulse response and then a tape measure and calculator. See if you can get any consistency between the different methods and if not try to figure out why and correct.
Once you get the timing sorted you can start with the crossover filters. As mentioned something is not right with the filters you have now. Good luck and have fun.