e3dV6 is not a good hot end for Bowden setup. The e3d Lite6 is better. The reason for this is that the PTFE tube does not go all the way to the nozzle in the V6. In the lite6 the PTFE tube extends all the way through the hot end. Look at these cross sections:
The issue has to do with retraction. For Bowden setup, you need to have a lot of retraction. The problem is that it will get caught on the edge of the nozzle as the filament comes back down. Over time, material will build up along that edge and impede filament flow and also cause the PTFE tube to pull out (unless you have the Bowden attachment for the V6).
Your best bet is to fork out the $40 for a Lite6. We use this hot end exclusively on all our printers. The V6 works best with direct drive as you don’t have to have as much retraction. And unless you’re going to print something exotic like polycarbonate, the Lite6 will work flawlessly for 90% of the filament out there.
I can’t speak to the v6 lite, but I can say that as someone who has printed hundreds if not thousands of hours with multiple e3D v6s and volcanos in a variety of heater block, nozzle sizes, bowden and direct setups, they work great as a bowden setup. The critical component is getting everything setup correctly and securely.
The bowden tube not extending down to the nozzle is one of the defining differentiators of the v6 from the v6 lite. It’s also what allows the v6 to attain higher temps and thus wider variety of materials.
The v6 and v6 lite have different end goals in mind and thus have a different design to accomodate that. It’s not a matter of the v6 lite necessarily being a better design or fixing flaws with the v6 itself.
I don’t disagree that the V6 is a good hot end. But if you are not going over about 280c, it’s not necessary. The Lite6 is half the price and can print pretty much any filament most people print. As someone who has printed thousands (if not tens of thousands 
of hours with the Lite6, I can attest to it’s value.
My Bowden setup issues were very similar to those the OP sited. Agree completely that setup is critical. The issue I was having had to do with the PTFE tube not getting seated properly against the metal tube that attaches to the heater block. It was almost impossible to get this right and as a result the gap caused the filament to hang on the edge of that metal tube during retraction. Considering the pressure you’re already dealing with in a Bowden setup, this added resistance was not good. Most likely the issue had to do with the clamp for the Bowden tube at the top of the hot end as well as ensuring the PTFE tube is perfectly square.
I have not gone back to address anything with Bowden setups since our direct drive setup is so reliable and easy to use. This thread has inspired me to take another look.