Switch off VR, at 1/1000s it's just causing problems anyway.
How much DOF do you have in this case? When you add a TC, you reduce the effective DOF on an already narrow DOF (FX). At F7.1 and a 2x TC the effective DOF will be half of DOF without TC? Right?
EDIT Okay, I'll back out of that statement, it seems after some googling that a lens with a TC will have the DOF of the lens it becomes e.g. a 300mm F2.8 + TC2x become a 600mm F5.6 with a DOF like a 600mm F5.6. I don't know why I got it upside down - so forget about that :/