Last week I was having some gnarly flickering problems with a timelapse. I got the plugin called "Flicker Free 1.01" by Digital Anarchy plugged into After Effects. I threw the effect on the clip of the entire timelapse sequence, the effect's preset was set to "timelapse" mode and I adjusted the "time radius" to "10". The effect adjusts the clips by itself and after that all the flickering in my video clip disappeared!
The presets include about 9 other options as opposed the preset I used, "timelapse". I bet ya there is a preset for your flickering situation.
Don't waste your time adjusting this issue frame by frame. It's not worth it. There is a plugin for you.