I know this may not be worth the effort but since it’s not a sped up video but a true Timelapse with many still photos, have you thought about taking the individual photos into photoshop and aligning each one so they are all “registered” and not moving around. You should be able to take a reference and layer it with each one as a reference, drop the opacity and slide the frame you are fixing around till it it matches, delete the reference layer and save. Then move into the next. You will end up with some black borders left over where an image was moved but just scale the video up slightly to get rid of those.
This can be very time consuming but may help you salvage a once in a lifetime Timelapse.
Naturally this assumes that the problem is that each image is slightly off from the ones next to it. *Not* if each image itself has motion blue from shake.
Bill