I disagree.
1) Warp drives do not actually move you at those high speeds and thus do not produce g forces in the ship.
2) Impulse drives are another matter but a drive which produces gravity might leave the crew in freefall even when under high acceleration.
When Enterprise makes a quick stop from high speed, all that kinetic energy has to show up somewhere. That would be heat in the structure. Just like car brakes getting hot.
Extreme heat shows up when you dissipate the energy of motion as friction. That's not an option in space, though--there are no brakes until you have atmosphere. You turn and stop the ship the same way you started it--with your engines. Since their energy obviously doesn't show up in the ship accelerating you it doesn't stopping you, either.
ST had structural integrity fields that kept the ship together, but that is boot strapping. The field generator would be tied to the structure and mechanical forces would appear at that point. Same with shields and deflector beams.
I disagree on the structural integrity field generator. It makes the material stronger, no force shows up at the generator.
You're definitely right on the deflectors and probably right on the shields.
Navigation is never really discussed. Captain Picard commands 'All stop!'. Within a few moments someone responds 'All forward motion stopped'. Relative to what?
I would assume the biggest mass in the neighborhood.