1200mm @5.6 with VR - Dang that is called covering some ground! There is nothing Faster than what you have.
I'm with Mike - I think she is talking about perspective compression as well.
DX - I've seen birders and some wildlife shooters do this. Part of the reason I'm not sure if I want to move off of DX as well.
Experience - I have never done a 400, but 300mm yes. With VR and a tripod I would stop it down to F8, auto ISO, Spot meter it and try to keep the shutter above 1/750. Exposure comp about -.7 to -1.3. Sharpness wins over iso any day in my book.
With VR I tend to go with a shutter that is smidgen under the focal length for DX to get decent shots. 1/2 a stop over the DX focal length to get better shot to toss ratio. With a 2x, depending what you are shooting, I try to go with the DX focal length at that distance if you can.
If you are doing landscape type shooting, stop it down to offset the converter (F5.6-f11 actual) and Lock the head tight, weigh the tripod down, Mirror lock up, remote shutter release, ISO 200, and take a shot at whatever the shutter is. Fire off at least 10-15 of each shot to hopefully get one without any shake into it. Keep the VR on as these lenses are designed for VR shooting on tripods. Consumer level one's are not. Take it slow, maybe 30-1 min between shots to take any vibration out.
I have never shot at 1200mm so maybe the compensation goes exponentially higher but that's what I follow.
Should be able to get some fantastic Full moons (that is huge in the shot) with landscapes. That would be a fun setup to play with!