I think you are on the right track.
A) This must be に because 止まっている here indicates a state where something exists, just like ある, not an action. If に were replaced with で, 止まっている would have to be understood as indicating a progressive action. Although that interpretation is not impossible, it is hard to imagine a scene where as many as twenty cars are in the process of coming to a halt more or less at the same time in front of a building.
B) You could use に here, but you would sound a bit like pinpointing exactly where the car should be stopped (and “exist” thereafter) as if the driver already knew the car should be stopped to begin with. The original sentence with で places greater emphasis on the action of stopping the car, and therefore, may sound more natural as an instruction for the driver of a moving car.
C) You can use に here. Although the same nuance exists as in B, it seems subtler possibly because the car is already stopped.
D) This に goes with 出る, not 止めた. It indicates a directional movement. The sentence with で would mean she stopped performing some action of “going out” in front of other people, which makes little sense.
E) The original sentence with に places emphasis on where the car ended up parked (or “existing”). Replacing に with で is supposed to shift the emphasis to the action of stopping the car. However, the resulting sentence still seems to emphasize where he took that action. This is because 建物の前で is inserted between the verb (止めた) and its object (車を), breaking the natural word order and making the inserted portion somewhat stand out.
The following sentence would sound more natural, or neutral, if the emphasis is intended to be on the action itself.