When I attempt to fill highly carbonated beers with the beergun I follow all the steps you have listed above....
Plus, as the level of beer rises in the bottle, I move the beergun rubber tip just below the liquid surface as the beer level goes higher and higher. Yes you still get foaming, but to me, it seems to help more liquid stay in the bottle. I also tilt the bottle at an angle a bit so foam can more easily run down the sides of the bottle when filling.
And yes, it does take considerable longer to fill a highly carbed beer, but it can be done.
I have also learned that pushing the limits with the beer gun and potential CO2 levels kind of peters out around 3.5 volumes or so. When I push 4.0 (or so) I get major amounts of foam and an undercarbed beer in the bottle. Almost better off to go a bit lower with hopes of maintaining the carbonation in the bottle.
Hope this helps a bit. Or at least gives you something else to try. Good luck!