I have a 2015 Mac Pro also with tons of externals without any type of problem as you describe.
After reading your post this is what I do differently; I don't connect any hard drive directly to the OWC TB2 dock except for temporary functions whether it be USB or thunderbolt. I will connect a usb optical drive permanently and that's about it. I just use it as a temporary hub.
I don't move my computer by twisting or turning very often because the thunderbolt connections can easily work loose.
I separate my connections utilizing the three thunderbolt buses and the 6 ports. How you connect makes a difference even in booting externals. I use two displays, an Apple thunderbolt and a Dell 4k these are on separate TB ports and buses. I have 5 thunderbolt externals connected but TB2 devices are separated from TB1 devices using different TB buses. So experiment around and try to pay attention how things are interacting.