Adjusting and matching time lapse exposure changes? (without deleting photo's)

Ok I am fairly sure there is no way around this but to do it manually... but just in case someone else knows a better way...
What's the best way to compensate for exposure changes captured during a long time lapse? (without deleting any images) (eg. a full day time lapse taken on a cloudy/sunny day)
Here's some more details...
I recently set up a 6hr indoor stadium time lapse during a cloudy/sunny day. All the settings were set to manual so that shutter (for motion blur), ISO, aperture (for depth of field) and white balance were consistent. I shot it in raw and it looks good... BUT every time the sun is covered by a cloud the exposure drops way down causing an overall 'exposure flicker' type effect when you put it all together.
So after searching for a while, I ended up manually adjusting over 1000 photo's, tweaking the exposure and eyeballing the histogram to be consistent (as 'Match total Exposures' didn't work in this manual mode instance). The result is 10x better, BUT I would love to be able to automate this process somehow as it would save me hours upon hours... any ideas? Any simpler ways?
The only automated solution I can think of at the moment is to set the camera to shutter priority in the future, but I'm not sure if the aperture / depth of field changes would cause problems when doing this.
Thanks for any ideas! I'm always learning and appreciate any input!

Codebreaker3 wrote:
I'm not sure that you will get good results if you try to normalise the exposure when dealing with large changes in luminance e.g. clouds moving in because that's the way the scene is at that time.
I understand what you mean, but in my case adjusting the overall exposures to be roughly the same made a huge difference and made the overall timelapse much better... 'smoother', less flickery to watch... it was probably because this time lapse was taken in an indoor stadium so the overall environment wasn't changing like it would in a cloud or nature timelapse. The problem was just that the overall stadium exposure would change according to the weather/clouds outside the stadium. I haven't heard of the Granite Bay Software so thanks for that link... I have tried LRTimelapse and it has a great feature to reduce the exposure changes for long term timelapses, but it also involves removing the images which have extreme exposure changes which is not what I wanted in this instance, I needed every image to remain in the timelapse. I think the manual method unfortunately is the best bet for this sceneriao, but I really appreciate all the ideas and suggestions!

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