Glad you got it working.
I'm trying to figure out what you've got going on. You're using the same filters for the woofer and the tweeter? I'm sure I'm just not awake yet but what you've got going on isn't making any sense to me. Are you breaking out L&R using mix channels in the PEQ?
Yeah, I'm with Nate, what's going on there? If you just attempt to correct the "whole speaker" response you're missing out on a huge benefit of bi and tri-amping which is that you can actually resolve frequency response ripples in the crossover region; if you try to make those adjustments "before the crossover" you'll have a hard time getting good correction because the "problem" is often with one of the speakers, but you're correcting both to try and fix it.
FWIW, the "correct way to do it" (insofar as there are any best practices in this discipline) is to EQ each stage (HF, MF, and LF in a 3-way) separately to get the best response. After the channel copy, if you're doing it all in PEQ the order of EQ vs. crossovers is irrelevant. All minimum phase filters will add up the same regardless of the order of operations
as long as you do it after the channel copying.
So you should copy the channels so they're all in the right places; then apply the EQ and the crossovers (in whatever order). To the extent you have the same EQ applied to multiple channels (i.e. to the extent that high frequency left and right have the same EQ), you don't need to enter them twice, just use the channel checkboxes in PEQ to select both channels.
None of this applies if you have a convolution step as FIR filters don't necessarily "add up" the same way; if you're convolving you should put the filter wherever it was in the chain when you measured it and tweak with PEQ afterwards to the extent necessary.