MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
allows you to interact with all your printers via the Cloud, and many other exciting new features.

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In Cura you can use the Tweak At Z Plugin. It's under "PRESETS", and is pre-loaded on the IIIP version, not sure where in later versions.
You just add a Tweak At Z layer for each temp change, then enter the new temp for each layer.