Thank you for sharing with us. You are experiencing a lot of frustration and I truly wish I could pay you a visit and help sort everything out! If you live near Chicago, IL, send me a PM and let's see what we can do. For now, here are some ideas I had.
I think I advised you incorrectly on the tuner pedal. The Polytune Mini 3 does not seem to have a mute feature when you engage the footswitch. This is why you are having issues. I read the manual here: [Invalid or Expired Link Removed]
A way to fix that is to purchase a separate mute switch or purchase a new Tuner that has a mute built-in. I use this one:
Mute Switch Pedal Guitar and Bass | Sweetwater
You are having issues with the Hyper Luminal Compressor - take the compressor out of the chain.
The Darkglass B3K, take that out too. Just a suggestion. What did you want to achieve with this pedal?
Try the Tech 21 BDDI as your main preamp and do this: set the Level the same as your bypass (bass only) level, Blend at 9 o'clock, Treble at 11 o'clock, Bass at 11 o'clock, Presence completely counter clock-wise, Bass at 11 o'clock, and Drive at 9 o'clock. That should be a good starting point with some edge to your tone, plus it will have a lot of your bass's inherent tone still coming through. Let the BDDI be your source of compression for now - it already adds it in when you use it.
What tunings are trying to switch to in a live setting? Please list all of them. Are you playing a 4 string or 5? How is your guitarist tuning between songs? Drop pedal? Other guitars? Perhaps you can transpose some of these songs without needing the Drop pedal so often.