Idk why I thought I had a JL w3 subwoofer, I just checked and its a RF T1D212 (it's the dual-2ohm version). Not sure what this means.The JL W3 comes in either 4 ohm or 2 ohm versions. Which one do you have?
If I had all the $$ that you have to spend on these equipment, I would run low level RCA cables from the head unit back to the trunk - i.e. you already have 1 pair in place, I would run 2 additional pairs. I would not use the factory high level speakers wires because a) I have no idea how the wires are run, how many connections there are, if they are installed in parallel with high current cables, etc., b) this is the most important - they are not shielded wires which means they can easily pick up noise. If you ran new low level RCA cables, you would (I hope you would) run high quality shielded cables to minimize noise.
I would initially set the subwoofer crossover at the head unit at 80Hz with 12dB/Octave to start. The crossover frequency and slope (12 dB/Octave is the slope) are greatly dependent on whether you're using a sealed, ported, or infinite baffle setup for your subwoofer. You may need to adjust this based on your taste, interaction with the Bavsound speakers, etc. That means you want to ensure you can adjust this easily without having to take the head unit out every time. Connect this via low level RCA to the trunk. Bridge 2 of the channels from your JL amp to drive this subwoofer. Here you need to be careful as the JL amp, in bridged mode, is only rated for 4 ohm. If your W3 is the 2 ohm version, the amp may not like it. It will work, but make sure you don't overheat/over-current the amp.
The next decision you have to make is how to provide crossover functionality for your door speakers. I briefly looked at the two links you posted. They are passive crossovers for Focal sets. Unfortunately there are two problems. 1) for the Bavsound speakers for the front door, you need a 3 way crossover because you have mid-base, mid-range, and tweeter. The ones on eBay are only two way crossovers. 2) The crossover frequency is unknown. You have no idea whether these crossovers are appropriate for your Bavsound speakers. You cannot just mix and match passive crossovers with random speakers and expect them to always work well.
I was looking at these 3-way crossovers:
These are rated at 18dB/Oct @600-4000Hz
These are rated 6-12/12/12dB (3/4/500/3.5kHz), except idk what bi-amps means
If these could work for my fronts, could I also run these 3-way crossovers for the rears and not connect anything to the tweeter section and use the mid and sub to split the Midbass (80-500) and Midrange (500-4k) at 5 like 00 or 600Hz?