I know that you said you're not particularly Video-editing savvy fmalover, but I do have a suggestion since you seem to be doing a stellar job.

Correct each individual shot as an image sequence (pick a single frame in the shot and then apply the same settings to each frame.)

Then save the corrected frames in a different folder with the same name/number as in the original.

At the end, you should be able to combine the new corrected image sequence to a video file easily.

Just a thought :)