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Have there been substantial further advances in the Warp Stabilizer in AE 6?
What would be "substantial"? No, apart from a few minor workflow and performance enhacements there have been no changes.
Also, has Mocha AE changed in any manner?
You still get mocha 2.x, just a slightly newer version, not mocha 3.
The main change with regard to mocha-AE is that it's more tightly integrated. You can initiate a track from within After Effects rather than needing to go out to open mocha-AE separately.
There are no UI changes in Warp Stabilizer for CS6. Bug fixes and performance tweaks, though.
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Thanks. Glad you like them.