Constant Frame Rate to Variable

As Mylenium says, you can't create variable frame rate videos like that with After Effects.

Also, while I think After Effects should allow higher frame rates in video output and in compositions, I don't really see the need for 90,000 fps. Would the human eye really notice a frame rate about 700 fps (or 1000)? Surely unless you would need to use it in a specific application afterwards, there would be no need. Nobody's monitor runs at more than a few hundred Hz - so for viewing on a PC monitor there's no need for any frame rate higher than the max refresh rate of current monitors (a few hundred Hz), and even in the next decade or so it is unlikely they will output in over 1000Hz.

You might be able to do that in another program though (but I really don't see much need to).

If you have a video with multiple frame rates, you could make the video frame rate the highest frame rate the place where you want to upload it/get it viewed allows. eg. for youtube you could set to 60 fps (though technically that would then mean any video within it that isn't a multiple of the destination frame rate would then have added pull-down judder added, but most people's PCs will mostly be approx 60Hz anyway..