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a) Select a clip in PrPro timeline, right-click and choose 'Replace With After Effects Composition'. Take care of handles if you might need them (that's rather general tip).
Warning about Collapse Transformation switch indicates that you have 'Scale to Frame Size' option enabled for your clips in PrPro timeline. If that was done intentionally, you can simply toggle the Collapse Transformation switch (small sun icon) off. If not, rather disable 'Scale to Frame Size' for your clips in PrPro timeline.
b) Quite a boring but covering almost all necessary details tutorial on basic work with Warp Stabilizer in AE CC from Adobe TV:
Some advanced techniques from Lynda.com
and Mathias Möhl:
c) When you're happy with your work in AE and going to lock it, render a digital intermediate out of AE, import it into PrPro and replace your dynamically linked composition in the timeline with that DI (see this good old thread on Dynamic Link workflow, pay attention to Todd's comments).
If you leave the 'Include Project Link' checkbox in the Output Module Settings dialog enabled while rendering your DI, you can easily get back to appropriate AE project so as to maybe tweak some settings: just select your DI in PrPro timeline, right-click and choose 'Edit Original'.
Mind the bloating issue, keep the amount of applied Warp Stabilizer instances in a single AE project reasonable.
Wow. Thank you so much Fuzzy. I'd buy you a drink if I could over the internet. Much appreciated.