Hi
i think your problem is that the animated psd is using the native AE PSR keyframes, and AE will automaticly interpolate the animation of those, and that is a very nice feature, but it sound like the other pre-comp you have is a sequence of images, that will ofcourse not be smoothly reinterpolated to a new slower animation, making the 2 comp not to sync up anymore.
One solution could be to bake the keyframes of the psd, as you have tried, but after that convert all the keyframes to Hold keyframes so that when you timeremap the master comp the animating psd will jump at the same timeinterval as the image sequence.
This can still fail though if you dont timestretch to a slow/speedup with an integer value (x2, x3, x4, or /2, /3, /4) as AE can put keyframes on "subframes" (frame numbers like 5,333) and with an image sequnce AE cant do that but will just take the nearest frame. This can cause some of the frames from the 2 comps to some times be 1 frame out of sync.
So keep the timestrech value to 50%, 100%, 200%, 300% etc. and you should be good to go... with an jumpy animation though :-D
Maybe i misunderstood you question, then im sorry for the lengthy response :-)
Robert