How to create a moving mask?

Hi,
I'm new to after effect, hope can get some guidances here.
I shot this time lapse sequence of Clark Quay, with camera panning technique, have encounter some issues to editing in after effect,
The panning is not smooth, as I need to adjust the exposure on the camera during the sequence. I presume can use wrap stabilizer to smooth it out, but I also need to blur out some of the building neon signage (Riverside point, Novotel and CQ Clark Quay).
My question is; since the daylight is changing, so are the brightness of signage changing too, and it moves too, how do I create masks to blur the selected areas, and they moving along across the screen?
Thank you so much.

The jerks in your time lapse are not going to be smoothed out by Warp Stabilizer. You will have to do some manual realignment of those frames to smooth the shot. The flicker in the lighting can be controlled by Digital Anarchy's De Flicker plug-in. If you want to selectively correct the color in certain parts of the shot you'll need to do figure out how to create some procedural mattes. Red Giant's Colorista II is very good at this.
Flicker Free
Colorista II
Both have tutorials.
You might also want to check out this great video from my friend Stu Maschwitz that shows you how to use Mask Tracking and Effect Tracking in AE CC 14.
Effect Masking - Mask Tracking

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