Try changing the frame rate of your imported image sequence.
Try turning on frame blending
Going from 9 seconds to 6 seconds is a 33% change in time. Without frame blending of some kind you are not going to get an even distribution of your original frames. Try 25% or 50% and see if that is smoother.
How would this work when using timewarp? Let's say I have a few clips and I'd like to alter their speeds at various points. Would I require a math degree to figure it all out? Is there no way to manipulate dynamic speeds of footage and then just have that render smoothly when it's time to render it all down to one movie?
Forgive my ignorance if I'm asking the world without knowing all the complexities of video.
Timewarp works no different than the normal time-remapping, it only offers more refined control and more sophisticated algorithms. since all effects in AE follow a WYSIWYG approach, you will always see the result of the remapping as you scrub the sliders, so I'm not sure what you are asking. If you ask for an mathematically exact formula or some overlay text that tells you "You are now seeing frame X", then that would have to be done by adding a linear counter in a pre-comp that matches the frame count and would then respond to the time-remapping as well. Otherwise I don't see much of a problem here, though of course complicated remapping back and forth can become confusing. that's why in such cases I usually split the clips into multiple layers and tackle one at a time, only taking care to match the in and out points. You'll get the hang of it, just try and don't let yourself be scared witless just because it looks complicated, which realyl it isn't.