Dust removal for macro shots

I find it very hard to make a consistent cloning frame after frame.

that is absolutely right. cloning is a hard fix for many removal problems since it is frame by frame, so inconsistencies between frames could cause a problem.

if the element/shot is moving, for example let's say there is a fly moving around the shot, or dust at one point in time and not the other, then you could clone from the same exact spot but from another frame in time where its not in that spot and paste when it on a frame where it is at the exact same spot - then the removal won't be noticeable.

on other cases, you might want to use a different approach, like stabilizing the shot/element first, then cleaning it with clone or other methods like exporting a frame to photoshop and returning it back clean, then re-introduce the motion.

since the particular circumstances in you shot - out of focus, perspective shift and so on - I would approach it this way:

1. stabilize the element in the shot - I used Ae's point tracker to stabilize this area

2. in the stabilized shot I created an adjustment layer with a mask and applied the "dust and scratches" effect (yes it's an effect for removing dust and scratches!), I found it much easier to render than Median and give the same result. just a few keyframes for the path since the perspective changes the shape of the area

3. precomp this composition and call it stabilized

4. copy paste the anchor point stabilized keyframes from the footage to the precomp's position and toggle the collapse switch so the boundaries of the footage won't be cropped in the master comp.

for the other dust elements you can work from with the stabilized precomp (they are in the same area and will be stabilized more or less)

here's the project to get you going:

DustRemoval folder - Google Drive